Hull down, on Thule Hullavators for me.
If you load from the side, hull down or deck down with padded saddles works fine, as do padded J-bars. If you load from the rear, hull down does not work unless you want to invert the boat after it is up, which I think is unnecessary. Loading from the rear generally does not work well with J-bars.
In very hot weather many people carry rotomolded plastic boats hull up to reduce the chance of the hull being deformed (oil canned). A bit of deformation on the deck is strictly cosmetic and will not affect performance. Over tightening the straps can increase the risk or oil canning rotomolded boats and causing cracking in the gelcoat of composite boats. With quality cam buckle straps, snug is good enough. They don’t stretch and have great tensile strength. Avoid ratchet straps. It’s far too easy to overtighten them.
If carrying boats hull down or on its side, a cockpit cover is recommended. It reduces drag and will keep your boat from ending up with a ton of water if it rains. Be sure that the cockpit cover has a secondary means of securing it to the boat in addition to just the cockpit rim.
If possible, support the boat as close to any internal bulkheads as possible.
I am a hull down kind of person. I don’t know why, but I feel that good saddles keep the downward force from the keel line.
Neither of my two long boats have an actual keel, but the bottom gets beaten up, sometimes a lot, so, like well set saddles that block further damage.
Neither of those boats are good at being set deck down. The flatwater boat is weaker deck down, or deck side. That is because the coaming is not meant for rolling. It is actually rather weak.
The surfski has too much rocker to sit on a J. It would cause all kinds of wind sheer, and I don’t need it.
I have a pair of Js and I haven’t seen a lot of boats that fit them right, I drive a pickup and have Thule’s an the bed, so they have about 4.5 feet between then.
There are many variables between boats and how Js are set that it is up to the judgment of the owner.
I bought (or, more truthfully, was sold) two sets of Thule J cradles when I re-started kayaking 15+ years ago. Over the years, as my boats changed, I too started seeing that some just didn’t fit very well. I gave away one set of Js but kept the other. Even though it’s getting old, it still works well for my rec boats (two thermoform and one poly) and leaves more room on the rack for kayaks that fit better in saddles (hull down) or my canoe that does fine with some padding on the cross bars.
J-bars work fine and they allow more boats to be carried on a narrow roof. However, they can be challenging to shorter people or people with taller cars that have difficulty in side loading, especially solo. J-bars can be difficult if trying to load from the rear.
It is best to stick to major brands when buying J-bars. There have been numerous reports of cheap off-brand J-bars breaking at the attachment to the mounting clamp.
I’ve used Yakima and Malone jbars. I prefer the Malones because they are easier to load. But, my Yakimas are old and they may have improved.