I think most people reverse the hood on the lens. If you need the hood in shooting
position just go with a larger case. I've got all the LowePro lens cases, many Kinesis,
Think Tank, and Tenba. Let me know what you want to store and I'll tell ya what fits what.
With hoods reversed or not, but with hoods is my preference. I don't mind a loos fit.
EFS 17-55 2.8 IS
EF 28-135 3.5-4.5 IS
EF50 1.4
EFS 10-22 3.5-4.5 (The hood on this one is real wide so I may be pushing it here)
I like an open camera bag with no dividers. I don't toss it around or give it to a flight luggage crew. I like to lay the cloths wrapped camera and attached lens on top of the stacked lenses in cases or maybe wraps.
Just me and my shooting style but if I have them in a divided bag, I have all these cases laying around. If I decide not to take a lens I have to pull it from the bag and case it.
In the case of WA lense hoods, I don't reverse them for the reason you mention (suffering from too-wide-i-tist) but set them loose in the case, at the diagonal over something else; where ever I can find room.