Some save games where this is especially egregious would be really helpful. I've seen some screenshots that are clearly not behaving as expected, so I know it's happening.
Locally, I'm seeing my fleets pathing through storms, though they do tend to minimize the number of jumps in storm systems if possible.
The behavior is tied to a define,
FLEET_PATHFINDING_COSMIC_STORM_WEIGHT, that currently adds 100 days to the "cost" per system that has a storm in it, but that shouldn't cause it to take a circuit around the galaxy instead of go through three systems. In my picture, if I sent the ships to Vurul it'll path around the storm, but if Baeeruta is the destination they cut across it.