Free thinker and freethinker, these two words may have two different meanings if you ignore the grammar construction. Most people will ignored the grammar construction in their daily conversation. So, these two words are having the same meaning. Precisely, free thinker is not a word,it is an incomplete sentence. It means the thinker is free. freethinker, free-thinker is a word.

You will primarily see "freethinker". You will sometimes see "free-thinker" (with the hyphen), which is acceptable. You will rarely see "free thinker" (two separate words); and if you do, it is not correct.

thinker, freethinker - noun free - adj amirite?

There's no difference. Both are the same and correct. (I should have written: 'I think, there's...')