Hello Shelly- I have a few questions:
How long have you had them?
If you got them in the spring and then they grew water roots, they would probably have a hard time making the transition to other media like bark.
I have read many times that when an orchid grows roots in one environment (say bark or air) they are sort of adapted for that environment. So theoretically if you took a bunch of aerial roots and stuck them in bark, they would "suffocate" because of the change in environment. Conversely roots that grew in water would dry out on a mount or maybe in a pot.
Now, when you say "dendrobium shoots" I think you mean keikis which grow on the stem of the plant and these will grow their roots in the air because they are elevated above the level of the pot. If this is the case, you are going to be putting air roots into a pot which could be a bad thing. The best time to pot anything is when a new growth is just starting to put out new roots because they new roots will grow into the new medium and will be fine growing in that.
Also- it seems that aerial roots actually seem to do fine when put into water culture (counter intuitive), but that is what I've read. I've never tried it myself.
Also when you say you have them in water, I am picturing them actually sitting in a glass of water, not semi hydroponics.
If you can post photos, it would give us a lot of information.
Anyway, when potting an orchid, you want to have a pot that is just big enough to hold the roots and one or two years of new growth, usually that is about the distance of the thickness of two pseudo bulbs. It sounds to me like these are keikis with long roots so you would end up with a pot that will be too big. Potting them up together would probably be best, but if you want to pot them individually, you can go ahead and use a 2 inch pot (way too big probably), but if you use giant sized pieces of bark or wine corks or some other type of medium that has a lot of air space and will dry out very quickly, you should be fine.