I've noticed some variation on warp speed at times, unrelated to any changes I've made. Seems to me there are certain places where you naturally go faster, but I haven't really figured out the pattern yet. One would think that those paths in sector space would do it, but I've never seen anything consistent there, though I've never done a consistent experiment myself.
The paths have no effect on speed; the original ideas for them didn't work out, largely because people objected to the wandering monsters drawing you into combat automatically. What's probably happening is a combination of the two different sizes of sector blocks, making it seem you're faster when in the smaller ones, and Diplomatic Immunity/Raiding Party (a buff placed on your ship by other players, which makes you faster in Sector Space and lets you enter the Klingon home sector).