No, that's a very bad idea. Expect it to break a lot of stuff. Potentially, yes. One thing I tend to do is merge mods that are only esps or where I don't want to copy assets (like say the extra esps in Weapons and Armor Remade), then include that merged file in a larger merge that includes asset copying. One problem with scripts is that some scripts will use the functions GetFormFromFile() or GetModByName(). These allow a script to look for the existence of certain esp files and possibly pull information from those files by looking up the form id in the esp. As far as I know, Merge Plugins can't or doesn't handle changing those scripts - especially if they're in mods you aren't merging. For example, I know from past checks that some mods reference Falskaar.esm and notice board.esp like this. If you use those mods and include those two files in merges, then those mods looking for those files will be broken in some way. Unfortunately I don't know of any reference that lists mods that shouldn't be merged due to this, other than the Dictionary in Merge Plugins.