All 40-9, unless specifically a conversion barrel, will have the barrel hood clearance issue. My 40SW Sig 2022 has 500 rounds through its 9mm barrel, but if I want to shoot 9 I bring a P320.
There are many here who've done the Shield-specific 9mm barrel in the 40 without issue, that I considered doing the same when giving my first Shield to my gf. A competitive shooter with an M&P (non Shield) 40 and 9mm barrel reported changing the extractor (due to chipping) 3 times, about 1-5k rounds per change, til leaving it chipped and still functioning as an extractor. He concluded it's an issue for high-volume use and wouldn't do it again.
Barrel to slide lock up I don't think is a big issue (on my Sig 40 w/ 9, accuracy did not suffer) as much as chipping the extractor.
My Sig's extractor is thick, my Shields... not so much. You're right almost everything is the same between the 40/9 slides, except the barrel hood width and therefore the extractor will be grabbing with "nails vs fingers."
Took pics of my 40 SP2022 slide with the 40 barrel and 9mm barrel.
40 barrel, slide, snap cap.
9mm barrel and snap cap, 40 slide
Shield 40 vs 9mm barrel
Debating on this very conversion, I ended up with a PC Shield 9 instead of a 40, but due to aftermarket barrel options now (Remsport, as 'serger' mentioned, and True Precision) I still consider trading my PC Shield 9 for a 40.
My last last concern is damaging the puny extractor on the Shield.
EDIT: Took these earlier.
Shield 9mm extractor:
Sig P320 9mm extractor:
Sig SP2022 40S&W extractor:
If the 40SW Shield extractor was as beefy, I may have given the 40-9 conversion a go, but from what I read they have the same part number.