The round Yak racks will be as strong as any other tubing, they are pretty stout. In that situation, both the Yak or Thule crossbars will flex regardless of square vs round. You've simply exceeded their limits. It used to be the case that the longest bars, 72s, were beefier than the rest, and we would buy those and cut them down for strength. I don't know if that is still true.
I've used Yakimas over the years, but consider both equals. Really depends on the specifics of your vehicle. The reason Yak used round tubing was to accomodate a curved roofline. In those cases, the round tubes allow the mounts to self-center and avoid stressing the system.
But most roof aps are relatively flat, so this is moot point, unless you have VW bug. The only design failure I've seen concerning round vs square is with the kayak mounts, as mentioned earlier - the Hully Rollers rotate under load when you slide the boats across them, which is miserable. I tried pinning the bars to the end towers, but no luck. I sold the hully rollers and downgraded to the basic saddles which work OK.
The boat mounts are the few that are single mounts, meaning they don't connect the two crossbars, like a bike tray or basket. Once you do this, you resolve any round bar rotation issues, as you make a solid, integral framework from the rack accesories and rack.
Specific to rooftop tents, or larger baskets, additional cross bars is your answer regardless of brand. Spread four crossbars under the tent system and you'll probably be fine.
m.
