Depends on how you do it. The plastron (bottom shell) is made the same basic way as the top shell (carapace), so if you cannot or should not do it on top, you shouldn't do it on bottom either.
While painting a shell overall is bad for several reasons, researchers and large-scale keepers have used latex and acrylic paints to mark animals for years. It wears off- and would wear off faster on the plastron (they usually use it over the tail on the carapace). The idea here is that the paint itself is relatively safe (no chemicals to affect the shell or system), and the relatively thin lines do not interfere with growth.
There is another guy on the forum who paints the tops of his torts shell. He said he had been doing it for years I think with no side effects. I think he breeds and does it to keep track of individual records. I tried to look up the pictures on here but I have no idea where it woud be...lol. I'm sure someone will be on here soon and know who it is.
I think the only caution when painting is to not put the paint or nail polish on the tender areas between the scutes, as that's where the tortoise grows. I think that as long as you use a non-toxic pen or pencil, you can write on the plastron. Are you wanting to have an i.d. on your tortoise?
I would never put nail polish on my tort, nail polish smells so horrible I don't like when my girlfriend wears it... All this stuff just seems so toxic. I know that too much sharpie on a human body can be toxic, so I would imagine at some level that would be true for torts (not saying the levels you are doing are bad, as I've written on myself plenty with sharpie)...