The answer is they didn't and because they had to, depending on which castles you're talking about specifically.

Keep in mind that a castle can range anywhere from this little piece of shit to this prickly bastard, with lookers like this beauty here.

Castles varied in size based on their purpose, the wealth of the owner/builder, their location, and dozens of other factors. If they had heaps of rooms it was either to entertain guests (so in a way to show off), for servants to live in (to run a castle you need a LOT of servants) or for storage and living for the family.

For the most part if a castle has tons of rooms, you should probably assume those rooms were being used by something, but when you think of the beauties in Neuremberg and Frankfurt, remember the tiny little motte and baileys that dotted Europe.

Which castles? In what time period? Where?

Obviously there's a significant difference in terms of intended use between, say, the 19th century portions of Windsor Castle and Krak des Chevaliers.

Well from a structural point of view: the larger the rooms the more complicated to construct. On lower floors you need a lot of stone walls to support the upper floors. So basements (which are often exposed in ruined castles) have a lot of small rooms for storage instead of one big basement like you would have now.