About the bug part: I posted an issue on the FAF github:
https://github.com/FAForever/fa/issues/2382.
Nukes are already flying at the highest altitude of all units. On their way up they first have to pass air units, then the novax satellites. And then on the way back down they pass the satellites and air units again. At least, if there were no bug that's what they would have done.
As for changing the trajectory in fancy ways, I don't think that's a good idea. The bug needs to be fixed and then the nuke will go straight up at the start, and straight down at the end. Changing trajectories will not change this goal and will only make them take longer to travel, which gives the SMD more time to build the counter.
Increasing the speed for this new trajectory is also not a good idea. The longer the total distance, the more that will change stuff. At this point you're working on a change for the sake of a change and you'll be looking at nuke behaviour from scratch. This is unnecessary. To add to this, if nukes go faster, anti-nukes will potentially have more trouble shooting them down. The physics in this game is still a thing that can ruin your day with that sort of stuff (think of PDs missing units because the units are moving in a particular direction at a particular speed. Different units but the same concept). I'm very reluctant to a change in the trajectory of the nukes to something more fancy of what we originally had.
Strogo, since you have the fix to the original behaviour of the nuke, could you post that as a reply on the issue I posted in the FAF github? Then everything can come together nicely and this issue will be fixed