One thing to remember is that this conversation is specifically in the context of Missions play, or at least my portion was. In a home setting, things have a lot more room to be custom tailored. In Missions, characters making foolish choices and/or not having appropriate licenses is (and should be) the primary barrier to being allowed to stroll around with the (insert thing here). Rolling down the street in a diving suit would definitely be odd, but it is not illegal at all. The same is true of quickened spells if you have your licenses. But sure, I agree, a chem seal article will not always be available or the best idea.
Unless you were referring to assensing, very few buff-related spells have an obvious effect. Prophylaxis is certainly not one of them. Element aura, armor, ect. are the primary culprits with a visible effect.
Mana barriers are problematic when subtlety is preferred. I also think that is perfectly acceptable. My Chicago mystic adept had a lot of stuff quickened on himself, and sometimes that meant I would sit out a portion of a Mission to not cause alarm, but this honestly didn't happen often. Many of the times we dealt with mana barriers it was boiling down to a fight anyhow. Rating 6 SIN and appropriate magic licenses got me through most of the "why the hell do you have so much magic on yourself walking down the street?" situations, but then again that character also ended with a 9 public awareness.
Personally, I had prophylaxis and natural immunity long before blight was a thing anyhow, because toxins in general are awful to resist. That's just my personal play style though, and there is nothing wrong with not taking that approach.
I don't disagree about run for your life. I just think the better game mechanic would have been to allow defense rolls vs. aoe instead of the convoluted work around. Then it wouldn't be necessary.