Your computer's performance is going to be affected by how fast the industries hardware standards increase as well as any running processes you have at any given point in time. Don't really give a **** how fast your computer is, I'll turn it into a Compaq Evo N800c with one dell installation CD.
On a more serious note though, Kevlar, the "Bloat", if you will, on your secondary HD is going to affect your computers performance the same as if it were all on one (With regards to your HD speed, once that's reached it then does matter). The reason being is because, any "Bloat" will still take up system resources. Unless you have that taken care of (By proper maintenance of course), then you'd still fall subject to bloat.