I think that for all practical purposes, how long it takes to clean a cage depends on the snake's personality and how likely it is to bite or to hit the floor running while you are doing cage maintenance. There are venomous snakes that don't give any trouble at all, and nonvenomous snakes that are a time consuming annoyance.
I do spot maintenance inside an inhabited cage with safety tools such as hemostats, gloves, scoops, plastic shields, etc. It only takes a moment to isolate the snake behind a plastic shield and pull the waterbowl by hand, or to use hemostats to lift the waterbowl out of the cage. I'd do the same thing for a nonvenomous snake that was known to be a pain in the ass or a biter. I think anyone would - nobody enjoys being chewed on as part of routine cage maintenance, or chasing escapees around the room.
I guess I'm just so used to the tools that they are a natural extension of my hand. I don't think that it takes any more time to use them than if I was doing maintenance on a nonvenomous snake cage. I worked in a facility where I did cage maintenance on a large number of nonvenomous snakes, and I really did not notice taking any more time in the venomous section. There were a few snakes in both sections that were particularly difficult to work around. The troublemakers in both sections got the same treatment. They did take extra time, especially the pythons. The big dread factor of that job was not any of the venomous snakes, but the %$#@ reticulated pythons that outweighed me, outmuscled me and didn't like me. I would rather catch ten cobras than clean one of those python cages again.
Fortunately most of my long term captives have habituated very well to routine maintenance, and they pretty much tolerate or ignore anything a keeper does. This is not to say that it is a good idea to put bare hands into a venomous snake cage or to get careless with them, but a reasonably calm venomous snake can be isolated behind a plastic shield, or tailed into a bin, or reached around with hemostats in a matter of seconds.
You're probably right in that those extra seconds do add up if you're talking about a hundred or more animals. But they'll add up just as quickly if you have enough nonvenomous "troublemakers" in the collection. I don't even want to think about how much more time it would take to maintain my snakes if all of my nice tempered long term captives were replaced by nasty retics or Asian rat snakes.
I think that a lot of people who keep hots don't handle them, which is a good thing - they should not be handled just for fun or play. Because of the manner in which I usually end up acquiring animals, I do have to go hands-on with them on a frequent basis during their veterinary treatment. Generally by the time they are fully rehabilitated, they are also well accustomed to handling and habituated to keepers working in or around the cage.
Because the consequences of a bite are so serious, it is never a good idea to fully trust a venomous snake even if it appears to be calm and nice tempered. **cough cough Gaboon vipers cough cough** But it's not hard to stay out of strike range using good safety tools and techniques, and once you're used to the routine it becomes pretty quick and automatic.