So, I had a planet taken over today.
1. Will I maintain a reference to the plant on my planet list (so I could try to take it back, in theory, at a later date)?
2. Does it affect my number of planets I'm able to occupy? In other words, can I now go colonize one of the many other unoccupied planets I have scanned, or do I just lose the slot?

Since it wasn't anything fancy, I might just let it go (I have better planets unoccupied already scanned); I just want to know how it all works.

yu can colonise a new planet
im not sure on how long it stays on scan but i have 2 old ones i let go
definitley colonise a better one

The planet stays on your list unless it gets fluxed

If you have better planets in que -- consider your self lucky!
I have several planets that I just don't want to pay 5GP's to get rid of. But I leave them completely unprotected and max out their resources. Hopefully someone (new player) will come along scan them and then take them.

If the planet taken was a good planet, and the person who taken is is about your level, you should take it back however, if the planet isn't good think of it as saving 5 gp