I have been working on an offline version of my Django web app and have frequently deleted model instances for a certain ModelX.
I have done this from the admin page
There is no issue, that's the way databases work. Django doesn't have anything to do with generating ids it just tells the database to insert a row and gets the id in response from database. The id starts at 1 for each table and increments every time you insert a row. Deleting rows doesn't cause the id to go back. You shouldn't usually be concerned with that, all you need to know is that each row has a unique id.
You can of course change the counter that generates the id for your table with a database command and that depends on the specific database system you're using.