I can't tell you on virtual Memory Cards because the number of times I've used that could be countered with a single hand...
But on a real memory card, PAL and NTSC-U save files can very often cohexist no issue. I have two Memory Cards, one for PAL games, one for NTSC, but on the PAL one I do have several NTSC-U save files, and everything works perfectly fine. And thanks to each region having a different character on the IDs, even different regional releases of the same game can be stored on the same MC.
A few games will give you issues, like the Donkey Konga games on my experience don't like that, but the vast majority of things I tried worked fine, and even then, I got away with having the Donkey Konga saves on the same memory card with a bit of a scrappy tactic (copy all the saves on the MC with GCMM, format the MC, start the Donkey Konga games, let them create the save files, and load the old saves back to the MC with GCMM again).
Now, if we were talking about NTSC-J (or in other words, japanese) games, then you will find always issues, as I guess for japanese save files you need a different character format than for NTSC-U/PAL, and thus a memory card needs to be formated to work with them.
With that said, it's never bad to make regular backups of your save files.