New server with 4 people I made 3 days ago has over 900k entities. These are not from playermade bases. can someone tell me commands or something to delete loot boxes/crates as a whole and remove horses/cars etc. I'm struggling here any help would be appreciated.

You can use this plugin to control this.
EntityReducer

I used the provided plugin but it only lowered my entities to 760k and seems to be climbing again. 

sounds like the actual game map - if its a custom map - use rusteditor and remove the duplications

You could use ObjectRemover