As another poster mentioned, frequently the room just simply isn't large enough for two queens, as opposed to the double-double that they have. That's a shortcoming of the property, where available physical space dictates the room sizes and resulting furniture. When the hotel was built, they could have either created larger rooms (read: fewer rooms in that hotel), or made them suitably smaller to have larger overall capacity.

Quite simply, many of these hotels are convention/meeting hotels, where room shares are quite common. (Cheapskate) Companies often request double-doubles so convention attendees or company employees can bunk two (unrelated) people in the same space as a single taking a room with a King or Queen. Convention planners are looking to maximize their room blocks and this is one way. You don't want to get into "attrition" as a meeting planner, but that's a whole other topic.

People also travel with kids, so these double-doubles are frequently connecting rooms with an adjacent King.

There are lots of reasons hotels do this, mostly because they know their target customers better than the OP thinks they do. If you want a bigger bed in a certain hotel, either request it, or frequent the chain often enough to increase your elite level (better chance for upgrades).