I have know idea how my mod accidentally ported over some fallout 3 only interior cells. I got megatoncratersidesupply cell and megatonplayerhouse and andaleoldmanharrishouse, 3 fallout 3-only cells.

All of them contain nothing.

Safe to delete by just pressing 'delete'?

EDIT: I also have a cell called museum of history entrance, with only a 'president door REF' inside it. I know I've never touched the museum of history while modding in F3 AND FNV. What happened?

FNV contains a large number of objects "left over" from FO3. I guess the developers figured it was more work to clean them out. First, you should make sure if you accidentally added them (which is possible if you merged things from other mods) or if they are just left over. If they are just left over, you should not bother deleting them. It will actually make your mod bigger, and make it less compatible with other mods.

To be sure whether you have added these items, one way is to use fnvedit. For any complex mod, you will need to learn this anyway. It will show you all the items which are in your mod, as opposed to being in the base game. Another way is to write down a list of the objects, and then run geck with only the base game file. If you search for the objects and they are there, then you should not worry about them.