If the lots you want to delete are in your Lots & Houses Bin they'll need deleting from the LotCatalog folder, if they've been placed in your neighborhood then you'll need to delete them from the Lots folder for that specific neighborhood. If they're in both places then delete them from both folders!
You can set Clean Installer to scan those folders and use that to delete them if you didn't already know that, it depends why you wanted to get rid of them from the folders instead of in-game, presuming you already knew you could do it in-game!
Maybe they're corrupt and crash when you click on them, maybe it takes you so long to load the game that you felt this way will be easier, whatever, you were on the right lines and know which folders you need to look in.
The empty templates shouldn't affect your lots one way or another and you shouldn't need to worry about those.
It will remove the lot, if the lot contained anything else like CC or hacks then they're still in your downloads folder. Clean Installer should help you identify those things as well. As in, maybe you'll see things you know came with the lot and that you didn't get for yourself. Or you can set Clean Installer to group things by date and that may help you find them more easily.