As part of asking about cleaning routine, I'd ask what disinfectant they use. I went one place once where she couldn't tell me what it was, just that it was blue and it definitely killed everything. I think anyone using a veterinary disinfectant will know exactly what it is they're using.
I'd chat about infectious diseases and get a sense from them whether they know what the common things are and how they can minimise the risk of it happening to any boarding clients (not putting bunnies on surfaces that can't be disinfected, e.g. grass, carpet etc, not giving them soft toys/rugs that will be used by other guests, that sort of thing). My pet hate (if you'll pardon the pun) is bunnies being put on runs on grass.
How clued up are they on things like referred aggression and how to minimise the risk of that happening. The number of photos I see of runs all lined up next to each other is astonishing, I hate it! Similarly if they move the bunnies from main accommodation into separate runs (again, something I don't really like personally), how do they do that, how much enrichment and security/hiding places is there in the run?
I'd also chat about signs of illnesses and satisfy myself that they can spot early signs of things not right and know what to do about it...and reassure myself that their vet is competent if it's too far to go to your bunnies' normal vet.