I don't see it. Almost any game world will have mages with fly spells and teleport other spells that can drop a NPC party of greater level then the PCs onboard their ship. And even if there's no active spelljamming community in sphere, the planet might well have a ship or helm lying somewhere the Gods can point to, or maybe the Arcanes would like to sell them one. Like any great warship, they can lay destruction down around them pretty well, but there are things out there that can take them out.
Fly spells are temporary and generally focused on the caster, and teleport spells are dangerous unless you're using the more powerful "teleport without error". Even then, teleport requires you know where you're going and can visualize it. A boat zipping around would be difficult to see and to visualize properly.
The big thing about Spelljammers is that they're pretty tough. If you compare them with Forgotten Realms Halruan airships (spelling?), the boats of Halruaa are finicky, fragile things.
While Spelljammers are slow (4mph per SR) it is a constant speed and they barely take any time to fly up and exit the gravity well. So with some math it might take a month to fly across the continent, but flying up and out into space, then back down towards your target would get you there in less than a day.
Then look at who's flying these things. They're usually high level adventurers. So lets say a dragon can manage to catch up with a spelljamming ship. It cannot flame it (it cant flame a target right before it while flying or it risks setting its head on fire.) but it can latch on and rip in with fang and claw. But doing so puts it in adventurer bitchslapping range. The dragon might take enough damage to knock it off but unlike a living creature, ships don't heal. That's one trick for GMs.
But the big thing is bombing runs. A long ship can load up on combustables, fly straight down on a city and not be seen until its too late (nothing else that flys can do so straight up and down.). They then dump their load, burn the city and fly off before resistance emerges. Dragons aside, only a scant few cities in d&d setting ever have truly effective anti-air defense systems.
By abusing the Up into space and down again loophole, PCs can also transport massive amounts of rare goods across the planet faster than all but the most powerful mages.
Basically, in the hands of an inexperienced and soft GM Spelljammer can ruin most settings. There's just no defense. In Forgotten Realms its actually noted that Waterdeep has no defense against them. Though Evermeet actually has a rather lethal one.
So by implimenting the rule that entering and exiting a planet requires a check due to high winds that far up, you limit how willing the PCs will be to abuse the trick and abuse their spelljamming helm.
