If your bunnies will be a bonded pair then I'd say it's really quite important that you take them everywhere together, always.
The most obvious time that they will travel will be to the vets. This can be very nerve jangling for bunnies at the best of times so it's better to keep a pair together for company and to give comfort and support, even if it's only one that needs to go - take both. When a bunny is poorly (except in particular circumstances) they will usually 'heal' better if they have their normal friend with them.
If one needs an op at the vet, then take both. Firstly, they will be less scared, but secondly, if you take one bunny from a bonded pair to the vets, that bun will come home smelling different and can very easily cause a bond to break down.
I would get one carrier that is big enough to take both bunnies side by side with some turnaround space and enough room for ears - particularly if they are uppy eared rabbits.
A top opening carrier is so much easier in my opinion. Most rabbits will hate being dragged out of the front door of a carrier and it's not the easiest thing to do. Taking a rabbit out of the top is much, much easier and less stressful for the bun.
What you don't want is a carrier that is so big that the bunnies can slide around when traveling. It needs to be big enough that they aren't crammed in, but not so big that they can get hurt if you stop quickly at traffic lights and slide across the floor.
If the bunnies your are adopting aren't bonded then you will need two carriers but the same guidelines would still apply.
Hope that helps a bit.
Helen