The "cat house" that I worked on, the lower 16" of all the walls had been sprayed by the cats, so it is entirely possible that your baseboards got hit, which is why I recommended sealing at least the walls, but every wall, floor, ceiling, in the rooms affected by the cats. Again, drywall is porous and takes on odors, so sealing everything is a necessity.

The carpet will have to go because there is no way to get the odor out of it once the urine reaches the backing or the padding underneath. When you pull the carpet you're likely going to see the staining on the underside of it and possibly on the padding. In really bad situations you'll see staining all the way to the subfloor under the padding, but really, if it got to the carpet backing, even if the liquid urine didn't go any further, the odor has, which is why you have to completely seal the subfloor.

What I would recommend is to strip the carpet and pad out of the room and assess the situation. You might be able to treat the subfloor with something like Natures Miracle or other urine neutralizer, which will reduce the amount of sealing you have to do, but it never hurts to be over cautious about it. Seriously, what's $50 in materials if you redo the entire room and can still smell the urine? An extra coat or two of sealer will eliminate all the odors, better safe than sorry.