The "consequences" are that you have to
A) navigate through them trying to time the travel through the clouds, dodging the one's with storms in them, or...
B) forgo the travel through the clouds and use the open lanes instead.
This messes with direct line travel, yes, but it costs NO extra supplies per day when you don't get hit by storms. It will however cost you more time travelling, ergo more fuel and some extra supplies due to more days spent travelling. It's now up to you to do the math and figure out if you would prefer the way around, or diving into the clouds gambling on getting hit or not, and if you get hit, if the extra supplies per day comes out as less then it would cost you to 'go around.'
Seems like a decent consequence to me.
Those "consequences" are completely inconsequential. In late game colony investments, capital ships as well as the target bounties and missions you do rank in the 200-500k range (plus significant scavenging resources which might end up your fleet with excess fuel after having stripped the wrecks clear). You can bulldoze through any storm and pay the difference because they do not matter.
I am never bemoaning the supplies or money lost, but the time me as a player wasted.
The bad thing is being thrown into a pinball machine which is simply a time waster which makes it harder to get to the exciting gameplay. As I outlined I am not fundamentally against some terrain dynamics, but they need to actually give you some positive feedback as well as negative risks to give you as a player agency and feel a negative outcome as being the fair result of some decision of yours in gameplay.
In pirates! that would be you chasing some galleon around the Carribean when you accidently clip a hurricane and now have your sails wrecked and speed impaired so running away from some privateer gets tough. The reason this kind of consequence feels fair is because that on map travel feels meaningful to get to the battles. You chase your enemies or your enemies chase you.
In Starsector all the meaningful gameplay takes place inside system at distinct locations (ABC) so everything in hyperspace is mainly idle time to get there. At best you may get a random encounter en route, but that is also no different from in system travel.
Hyperspace currently does not feel organic in how those clouds are placed, ships travel in or around it or how they interject into a player'splans. They are just something that wastes a players time before he can have fun, be it battle, trading, colony management or simply outfitting your ships.