Don't overthink this. I gather you're shopping the bike vs. just the wheels. In that case, assume the wheels are roughly comparable to the frame and other components.

Consider that wheels generally get replaced/rebuilt a few times over the life of a bike that's well used. So, focus on the commonality of the dropouts, brake mounts and other critical points on the frame. Then, if all checks out, go ahead with the expectation that the hubs will outlast the wheel, and that you may upgrade if/when the need arises in a year or two (or more).