To answer your specific questions:
So what is the difference between an internal hard drive and an SSD? Is one preferable? ----- SSD can be external or internal, the comparison is a spinning disk or a SSD (explained above quite nicely). I prefer SSD for music, no possible noise at all. In theory SSD are more reliable, but you should have backups anyway.---
The manual suggests using either a 3,5" or 2,5" drive. Does size matter ? ( no pun intended) -----No. However 2.5 are even more expensive then 3.5, so unless there is a technical/space reason given by the manufactor (maybe you can fit two 2.5's and only one 3.5 for instance) than get the 3.5 SSD.----
Are there sonic differences in the different available brands? ----I've used many brands, I have not heard a difference, and there shouldn't be one with an SSD. I just go with the one that has the best warranty and specs for long life.----