If you can't kill something with overwhelming power and kill it relatively quickly, you shouldn't be attacking it. A scenario where you attack a superfortress and your entire attack force gets killed, but you damage it to 50%, and then you send in a 2nd force to finish the job is a very inefficient use of resources.
You should attack with more troops and kill it the first time. If you can't do this (lack of force cap), you have probably already lost the game, as while you are clearing this chokepoint, the AI is preparing a new and even bigger one somewhere else.
If find this not to be true at difficulty 7ish and down. Perhaps at the difficulty 8 and up, but at difficulty 7 it is quite reasonable (and often necessary because of ship caps, the position of your fleet for defense, etc), to take down a superfortress or similar in multiple waves, rebuilding in between.
This also comes back a bit to larger strategic choices in general -- I tend to have Mark II Command Stations and focus on high-yield resource planets, etc, so I tend to be quite rich in resources, with ship cap (usually) being the greater limiter if I play too conservatively. So in those cases, there is an impetus to get things done quickly while still maintaining defenses around my wide perimeter of resource-valuable planets. I tend not to be holed up in a sector of the galaxy, but rather strung out as needed to get what I want, so massing my entire fleet at one point is almost never possible. Meaning that I have no choice but to assault a Mark IV planet with a superfortress with just a third or less of my forces, for instance.
I'm not saying you are wrong -- in your style of play, and at the difficulty level you play at, I am sure what you are saying is spot on. I'd just caution against blanket advice of that sort, since the playstyle of an individual player (and difficulty level, to another extent) can really have a huge impact on the strategic imperatives in general. In my games, perimeter defense is challenging and and ever-present threat, but resource efficiency is vastly less of a concern than it is for you. So the smartest choices in how to assault an entrenched target necessarily vary, then.
When I'm at cap with a ton of resources pouring in, and I can't move big parts of my fleet for risk of losing valuable territory, it only makes sense to hit a superfortress with a third of my fleet, quickly rebuild that, hit it again, and repeat as needed. In a temporal sense, it's extending my ship cap based on my greater resource income, which I require a greater (temporal) ship cap in order to defend.
Anyway, so I think that's where the differences lie, is in fundamentally different playstyles (which I think is too cool, incidentally).