I don't know of any ships that have two distinct bedrooms; but then I never looked for one. The suites I have seen (notice I said seen, not stayed in) have one separate bedroom and a combination of pull-downs, sofa beds and roll-aways in the sitting room.
Princess has a catagory called 'Family Suite", which is two inter-connecting mini-suites. but there are only two on each ship, so you would have to book way early.
Another possibility would be simply two adjoining mini-suites. You wouldn't have a connecting door, but the partition between the balconies could be removed giving you one large common area.
But as I said, I'm not familiar with all lines. There may be one with just what you are looking for.