No, I seriously doubt it. I am going to continue using PJ64 v1.6 because I don't like the extra input latency that comes with the Mupen64Plus GUI option. Whether or not the latency is the same and I am just perceiving it to be different, I really don't know. I'm just too used to PJ64 to switch at the moment. And... it took me a while to set up the PJ64 EMU properly with all the best plugins. I am not keen on repeating this process with a Mupen EMU.
From what others have told me, these vulnerabilites have existed for many years and this isn't a completely new thing (I think PJ64 v1.6 was released in 2011). It doesn't really concern me as I will not be downloading random ROMs and ROMHacks. I have all the ROMs I require already.
Please someone let me know if I'm wrong about any of this.
As far as I'm aware the rules have changed for this. I've been using Mupen64Plus for all my runs and they have been allowed for submission. It states in the rules that Mupen64Plus is allowed for any operating system, but that PJ64 1.6 is the preferred emu of choice. So as long as you're using Mupen64Plus and not Mupen64 you should be fine here. I assume people are wanting to use newer versions of PJ64, but what I don't understand is why not many emu runners play on mupen - is there a disadvantage to this that I am not aware of? Does Mupen64Plus somehow run slower than PJ64 v1.6?