Cheating Sigwulfe may cause some minor weirdness.
If you're buying them, it actually just sets a flag, so the next time you're on your ship, you get a "setup"-sequence, where you name it and stuff.
Pretty sure that doesn't trigger if you just buy it.
I'm also not sure what would happen if you cheated Nova/the goo armor. Basically, items that are also NPCs are kinda iffy.
There are also some quest items that you can't place in storage, but which also don't take up inventory, either. Cheating those might cause issues, since they're essentially quest flags.
But regular items, even if they're "unique" or "pick one"? No issues, really.