All of the level gates we know of are pretty low, and level doesn't seem to affect aptitude at all. It's implied pretty early on that levels are mostly (but not entirely) just for show. Also as you said, Annie is a serial grinder, whatever the level req is for the nuke, she'd absolutely have already reached that offscreen, especially since the party had already killed quite a few xenomorphs at that point.
I guess the other thing is that we don't really know whether the level 2 requirement for magelight is for use or just for learning, since that isn't fully explained. If it's for use then that means the nuke would require her to level back up to use it, but if it's just for learning it then she'd only have to have learned it once when she reached the req. I think level req for learning rather than use makes more sense as far as Eternum's magic system goes, since skill and aptitude aren't necessarily based on level but rather affinity with the game system and individual experience. Major spoiler: This also makes the most sense with what we know of the world of Eternum as a whole. The true multiverse doesn't care about player levels at all, they're likely just a means to gamify the multiverse experiment and maybe keep people with low affinity from getting too deep too fast. The actual use of magic in Eternum would be based off of the user's skill rather than an arbitrary number that only the neural implant cares about.