Please don't tell me it's code to do so...is it?
Of course it is legal to do so...
I can't speak to structural degradation, but I can't imagine how Swiss cheese is worse than a big whole. My gut feeling is that a bunch of half inch holes a half inch apart cause less weakening than a single large hole.
I've pulled NM out of joists where the holes were sized and
shaped almost exactly to the oval shape of the cable.
Of course, 12-3-G fills a round hole nicely.
Let's just say that I lean toward Swiss cheese as the preferable way. I think so long as I'm leaving 60% there, it's structurally safe.
If you are making a single hole up to 1.5", I wouldn't object, especially if you are restoring it with steel.
Perhaps you need a faster drill or a sharper bit.
It's easier to trace wires through Swiss cheese than in a bundle, but a little harder to protect with plates.
No derating in Swiss cheese...