It was just filling his character out. Perhaps all of his Species are like that or maybe just him.
It was kind of a character gimmick really. Another Doctor wouldn't have had all that crap. I think it was kind of a hobby for him.

I took it that at this point in time medical technology was not as advanced. Phlox used natural medicine from his creatures. Really it was just a fun gimmick for the show which I enjoyed. "A Night in Sickbay" is one of my favorite episodes.

Wouldn't it have been easier to replicate or manufacture what ever he was getting from the animals.

He used some of them to cure or treat various ailments, but some of them were just food for the others.