If I read the question correctly you are asking if you can do something like drill a hole in the driftwood or cut a piece off and glue it somewhere else…
Drilling holes in it to create a cave shouldn’t be a problem at all. You will want the wood to be completely dry but that is to make things easier for the drill bit or saw blade, not to protect the wood or fish. After you cut/drill it simply rinse off the saw dust and there ya go…
Regarding siliconing… I had an experience once where I siliconed shelves into an aquarium to create a terrarium and left the silicone to cure for 72 hours (the label said cures in 24 hours) I still had major problems resulting in the death of several fish. Silicone cures as a chemical evaporates out, so the less surface space you have open to fresh air the slower it cures. So whenever we use it to glue to things together we have very little exposed surface space it it will take a very long time to cure.
I have used an aquarium grade adhesive that dries very quick and is made for gluing fish décor. I don’t remember the name but it is a green substance that is sold at some pet stores and comes in a 9 inch long 1 inch diameter tube. For gluing I would suggest this stuff over anything I’ve found, for sealing, nothing beats silicone.