In some cases, I find that you even HAVE to use the real SID in a remix, or it will fail utterly... this is especially true when complicated ringmodulation, sync effects or waveform combinations are involved in the original, that simply are so unique to the score, that it's unavoidable to use it simply because no synth other than the SID can create that sound, or at least it is so horribly impossble to analyse how it was created.
Some tunes with this that I can recall are as mentioned Sanxion, that has a destinctive rythmic feel that is heavily effekted, and making any remix without it would not bring the "soul" of the tune.
I had this problem myself when I remixed R1D1, which is why the heavy synced sounds after the main melodylines is actually sampled directly from a 6581 SID chip (effects processed afterwards naturally).
Summa Summarum; I'd use SID sounds if the remix would loose the originals "spirit" without it... only when moderns synths can improve the experience will I use them (which is fortunately most of the time hehe).
In fact, many of Hubbards tunes have these weird rythmic effects that call for it... he had a tendency to ringmod and sync melodylines with rhythmic parts rather often, and I believe he probably had much fun just "switching these on" to see what random useful things he could come up with
