I'm a big fan of clear slotted pots for phalaenopsis. When you repot them you can cut off any roots that have grown out through the slots. It won't hurt the orchid. If you wish to save those roots you can cut up the plastic pot instead. But of course that ruins the pot.
The roots should turn green when the plant is watered and turn white as the medium dries out. But if the inside of the pot is turning green then you do have algae which is pretty common with clear pots. I don't know if it will eventually become a problem or not. Flushing the pot well, once a month will help flush out excess fertilizer salts and letting the medium get a little drier between waterings will both help control algae. I use Physan 20 at a rate of 1 teaspoon per gallon, once a month to control fungus, algae and bacteria. It doesn't completely eradicate the algae but it does keep it under control most of the time.
Since I always use clear pots, I can't answer the question about moving them back into an ordinary pot. I would imagine that it would probably be OK.