Changing the tubes on a SV will change the tone, as it will on any tube amp. However, the tube amp in the SV series is intended to be pretty transparent. The SV series uses full amp and cab models, meaning that the pre-amp, power-amp, and cabinet is fully modeled. The tube amp is just coloring the tone on top of that. It may not have as drastic of an effect as changing the tubes on a regular tube amp.
For example, the 12ax7's in a regular guitar tube amp are fully involved in creating the unique sound, whereas the 12ax7's in the SV are there simply to boost the final fully-modeled signal before it hits the power amp tubes. So, changing the pre-amp tubes on the SV may not have the same amount of effect as it would on a regular tube amp.
When I got my SV, I put in a pair of matched JJ 12ax7's. They were a bit darker, and had just a bit more break-up at volume. I set up all my patches using those, and it sounded great. So, when the time came to change 'em out, I just stuck with another pair of matched JJ's because I didn't want to adjust all my patches. Same for the 6L6's. I used the stock ones, and replaced them with the same.