Questions about Sims 2 Files

I delete the Accessory and Groups caches almost every time I finish playing, or before I start up the next time. I occasionally delete thumbnails from the Thumbnails folder within Legacy and the Thumbnails within each neighborhood. Within the Logs folder you can also delete all of those. Any of these files can hold onto outdated or unnecessary information or become corrupted, or just take up space as they grow.

The game will generate new files as needed for all of these when you start up again. 

What absolutely cannot be deleted without some work in SimsPe, and with batbox and hoodchecker, is the character files. The ones like N004_user00000.package and the lot files like N004_lot00.package. Those are Sims and Lots in your game. Deleting character files would result in Sims without any information, causing corruption. Some of the lots might be okay if you deleted them, others are tied to Sims that live or lived there and you'd be leaving behind references to something that didn't exist anymore, again causing corruption. 

If you really want to have fewer of those types of files you either need to download and install cleaned neighborhoods (there are some out there available, like those from MeetMetotheRiver) or aquaint yourself with the needed programs and do the appropriate steps yourself. The easiest thing to do obviously, is leave them and deal with it.

Why does it make so many if there is not that many lots or sims

Because there ARE that many. The extra lots are lots in the bin. You can delete those from the bin, but the files will still be in that folder. And if you create your own lot, then decide to delete it, that file will still be in the folder.

 The extra character files are dead pre-made Sims (many of whom are missing gravestones unless you recover them), the ridiculous number of townies and stray animals the game produces and duplicate NPCs. I don't know why, but the game generates three maids, three unsavory charlatans, 3 mail delivery persons, 3 handy persons, 3 dog trainers... and on and on. This stuff is why I learned to make clean neighborhoods myself. So I could have one maid, one cashier, etc. and fewer townies and strays. I also installed an anti-redundancy mod, an anti-townie respawn mod, and an anti-stray respawn mod, so they won't come back unless one dies. I also have a "there can only be one professor" mod for when I generate a college neighborhood, because it will generate a bunch otherwise. Realistic... maybe, but not necessary.