It all sounds very dangerous!
Not sure there technically
is a surface for a gas giants so landings are out of the question there anyway. It would all be about the pressure.
It wouldn't just be an issue for gas giants either. I saw a screenshot the other day of a rocky world with a silicate vapour atmosphere where the pressure was 10 million atmospheres (IIRC).
Besides, spaceships are built to hold a pressurised atmosphere in against a lower external pressure, not to withstand a higher external pressure. None of our existing ships would be able to cope with anything much beyond 1 atmosphere. Throw in wind and turbulence and even for 1 atmosphere, planetary landings would be a very risky business for most ships. Wind shear in gas giants would be a huge problem too.
So it's either going to need specialised ships, or very very drastic modifications to existing ships (and it'd probably still be too much of a stretch for a lot of them.) I'd say the most probable scenario is going to be small ship launched atmospheric vessels and a few new specialised larger ships that aren't going to be very effective as actual spaceships. Either that or new shield tech, far beyond what we've currently got. (If only there was some ancient extinct race who had shields much better than ours whose tech we might eventually be able to access and use..

)
The situation's worse for underwater. The pressure's much higher compared to the relative atmosphere, plus additional propulsion mechanisms would be needed to travel through a liquid medium.
I'd love to see the Moray Starboat in game at some point though.
Anyway, personally I'd much rather FD did a good job of it all and took all this kind of stuff into account rather than rushing it. Definitely seems like it'll be a good while before this would happen though. We'll probably all need a bit of a platform upgrade to be able to run the game at the quality we want when all that comes anyway so a bit of a wait's probably a good thing.
Edit - Ninja'd by GreyArea on gas giant landings!