I totally get that. And like I said, whoever wanted to keep them together probably had only good intentions.It's a very different experience watching a bonded pair. I think "having a bond" and "bonded pair" are two different things, frequently confused.
But a shelter must be a stressful, scary place for cats, or any other animals. This is just conjecture, but I could imagine animals bonding and sticking together when living in a shelter. For comfort and survival reasons.
But there's never any guarantee that will continue after moving them into a larger space, where they can naturally exist as cats. I'd certainly hope they'd continue to get along, but there will always be a possibility that the situation doesn't work out.