Loosely ordered within sections with fastest first. I haven't actually tested these to see how fast they really are, so these are just estimates.

Finding a secret will instantly finish the map you're on, the same as if you had killed all the red guys. You can only find any given secret once, though. The best time to use them is, in my opinion, anywhere from nodes 6 through 7c and on lost / powerless (that's the one where you don't have hacks anymore). Using them on more difficult levels is better, as more difficult levels must be played slower, and it reduces your risk of dying.

Most viable in runs, largest timesave

Lab - In the level, right behind a starting position.

Canals - In the level, under the bridge.

Yakuza - Behind a fake wall in the bathroom, second stall. (next to a starting position).

Island - Near the indoor staircase, you can jump onto a beam to get behind a bookshelf. Secret is right there.

Platform - Throw a monkey wrench at a wide pipe on the side of the map that's far from the computer room. Secret rises up, watch your back as it cannot be collected until it stops moving.

Prison - In the corner, there's a table on its side next to a locked door. Shoot the lock, and it'll open to let you at the secret. Big timesave, prison is slow.

Morgue - Grab a fork and throw it at a (concrete) dead body, the glass shielded area will have a door open for you.

Still very feasible, but slightly riskier/slower

Kitchen - Grab a fork and throw it into the electric socket in the freezer room. The door right next to it will open.

Parking - Grab the credit card/keycard from the payment desk on one side of the level, throw it at the rectangle shape next to the fence that blocks you from the secret. Takes a sec to rise up, but you can hit it from where you pick up the card.

Bar - Grab the only painting, throw it at the dartboard across the room (near the pinball machines). Fence blocking secret (behind back of the bar) will open.

Library - Underneath the balcony with the broken railing, grab a book from lower down. One of them opens the secret bookshelf when it breaks.

Corpo - On one side of the map, outside of a window, there is a massive funnel made of chairs. Land just off the center, without going through (going through puts you back in the map again, no big deal).

Subway - In the front train car, you can hit a button next to a door, and it'll open. Go all the way around to the front of the train to get the secret.

Gym - Grab a syringe from the bathroom, throw it at the statue nearby. Secret opens in the bathroom (i think)

Casino - Three slot machines have throwable levers. Break all of these and the secret will open up on the opposite wall.

Station (Takes a while, but this level is slow, so it saves time) - Grab a gas/oil canister from all over the map, go to the left from looking out from the store. There are a couple of things you can jump on to make it over the fence. Once you're over, head left, to the back of the station. There'll be a car blocking the secret, throw the gas at it to make it move out of the way.

Sewers - Grab one of those wheel valve things and throw it at the weird spot on the overhead pipe. Secret opens up right in front of you.

Dojo - Throw the fans on the wall at each of the samurai statues. Secret will open next to where the fans were.

Studio - There's a crumpled tube of paint near one of the paintings on the lower level. Throw that at the center of the nearest canvas, and a door will open up behind you. In that room, pull the painting off the wall to reach the secret. I'm not sure, but the paint throw may be fairly precise.

Reasonable, but riskier or slower

Definitely practice these before trying them in a full game run. Or don't, I guess. Some of them are only viable in certain spawn locations.

Tower - You'll need to time a jump onto the bell at the top of the tower, so you can climb up on top of the bell. Secret is right there. Practice this one! Most viable if you spawn at the top.

Containers - There is an unopened container above where the toy spill is. One of the platforms you need to jump on to reach it has a crowbar, grab that. Throw it at the widest side of the container. You're in the open doing all this, be careful!

Garage - Grab a hammer from the workbench behind the hanging engine and throw it at the spot where the screwdriver is stuck in. The door will open over by the closer staircase. Only viable if you spawn near the hanging engine, otherwise, you'll have too many enemies to deal with.

Bank - There are two credit cards/keycards, each one near or on a bench. Throw them both at the rectangles next to the vault door (not the spawner one). You may need to throw one at the left and the other at the right side. Vault door will open.

Chapel - In the graveyard, jump onto the top of a grave, and get to the fence. From there, get on top of the building. The secret is a little higher up, you'll need to get to its raised position by jumping onto a corner of its platform.

Site - Jump up on the truck (a little tricky) and go forward and to the right, around the wall and there is a (kinda long) path straight to the secret.

Office - Grab a pay phone (without antenna) from in the office, and go out the windows that have less ground. Go into the phone booth and carefully throw the phone directly at the receiver, the throw is a little precise. When you do, the secret will appear some distance behind you. There'll also be a surprise, but nothing that'll throw you off.

Disco - Throw a record (it can be the same one three times, or whatever your heart desires) at the turntable three times. Massive door behind turntable will open. From there, platform to secret from the right side. Doesn't save much time, only use if you spawn at the turntable. If you're a gen x-er who doesn't know what a record is (after all, the millenials and gen z know because records are cottagecore or something) they're the flat discs.

Probably not useful, too risky and too slow

Sawmill - May be useful, but risky and slowish. Shoot the lock on the locked fence near the knife book. From there, go out and jump past the moving saws to get to the secret. You can one-cycle the saws, but I believe they one-shot you if you hit the sharp side. Can save good time, but may not be worth the risk.

Mansion - There are two strats. One is much faster, but really precise and I could only hit it once in several minutes of trying. Slow strat: break aquarium, throw fish until "GREAT IDEA" flashes on screen. Jump over to the left balcony (looking out) and climb up the stairs to the secret. Fast strat: Go to the right balcony, land a jump onto the slope between balconies, from there land a very precise jump onto the spawner that's sticking out on the right balcony, and then you can reach the balcony cover, which gets you straight to the secret without the stupid fish. Probably not viable at all without some reliable setup for what I'm calling nerbfish. Doesn't even save much time, Mansion is a fast level.

Corridors - Just slow, about as fast as beating it the usual way, by my estimate. (Although I may be wrong.) From the left staircase looking down, jump onto the palm tree, and then onto the top of that staircase. From there, go over the top of the upper side of the level, to a long bridge which eventually takes you to the secret. It might have some usage if you're low on health and want to minimize your risk of getting hit.

Helipad - Slow, like corridors, but you can also be shot at. Go up the long stairs and hit the button behind the pole. This lowers a chainlink fence back down in the main area's upper level, allowing you to access the helicopter and the secret. Almost harder than just killing, even if you know how to do it.