Couple of things.

First, the patrons never put the tables and chairs back where they're supposed to be (even if they try, they get it wrong), so the minimum-wage waitress/busboy is stuck with the job of rearranging furniture, and cleaning up the floors. This is one reason that large groups get the "mandatory gratuity" treatment.

Turnover: every restaurant needs to turn over tables on the regular. If a large group is sort of lingering even after being decimated, and the diner can't reclaim those 4-tops for another party, that's potential lost revenue.

[Hmm, is that how "The Four Tops" got their name?]

Wait staff are often assigned "stations" based on a group of table numbers, so if you shove together enough tables for 12 patrons, you may have a conflict of 2-3 waitresses, but only one "main" can be allocated.

Any table or chair that can be lifted or moved by a patron becomes a potential melee weapon. Diners are occupied by rough crowds and after-club drunks who are trying to sober up. This is also why you're lucky to get a butter knife with your sirloin.

Booths feel more comfy, and offer a better feeling of privacy than tables. A table's more flexible if you have a family and toddlers, a wheelchair, or something, but booths are for lovers to cuddle.