Since Any% speedruns skip turning Manannan into a cat, they must avoid getting zapped by him on the pirate ship. There are several things that make this possible: 1) Manannan won't appear if you're carrying the box; 2) Manannan will take some time to appear if you switch screens; 3) he won't appear at all in the small outdoor area at the stern of the ship, to the left of the captain's cabin.

If you waited for Manannan to leave on a journey, an additional rule applies: once you board the ship, Manannan won't appear until the seconds on the game clock show "04 (after the first "04 on the ship he can appear at any time). This makes it easy to dodge Manannan just by boarding the ship at a good time; for example, if you board the ship with the game clock at 0:10:05 you have a whopping 59 seconds to get the box, drop it in place, jump up, climb the ladder, open the chest, get back your stolen possessions and head into the safety of the stern without needing to worry about Manannan at all. Even in less favorable circumstances, though, it is possible to reliably avoid Manannan; this is accomplished as follows:

1. Zip to the eastern part of the hold (a screen switch) at Fastest speed, and then get the box as quickly as possible. (From your starting point in the hold, one possible series of zips is 926724 GET BOX.) Manannan will not bother you while you're carrying the box, so you have some time for a deep breath.
2. Zip back to the western part of the hold (84), take the aforementioned deep breath and prepare your next command (DROP BOX) without hitting Enter yet. (Waiting in the eastern part of the hold is an entirely valid alternative; but waiting in the west may help with getting oriented, since that is where the action will happen.)
3. Be ready for quick action. Switch screens twice (64) as quickly as possible to buy some time, then immediately follow with 26 DROP BOX [] JUMP F3 [] F3 [] JUMP LADDER [] F10 (this switches to Fast speed - you cannot climb the ladder in Fastest), then 8 to climb up the ladder. If the captain is in his cabin, climb back down and up until the cabin is empty.
4. Save here, in case of a bad ladder exit. Carefully leave the ladder, then switch back to Fastest and make a dash for the stern. Ignore the chest for now. One possible way to zip to safety is 49271.
5. Take another deep breath, prepare your next command (OPEN CHEST) and be ready for quick action again.
6. 6272 OPEN CHEST [] GET ALL [] 79271. You can now wait out the rest of the 14-minute journey without worrying about either the pirates or Manannan.