Does using redstone cause a slowdown when using a fill clock?

Solution 1:

Yes it does

This article goes into quite a lot of depth on the matter but the main point is that while redstone dust does not trigger lighting updates, it does trigger redstone propagation updates, which are just as bad! Wherever possible, redstone dust should be eliminated from clock circuitry, or any circuits that are running very frequently. Use fill strips instead to power all your command blocks.