Yes, having a large number of jobs just sitting there defined but never used could have some performance impacts.
Things like autorep -J ALL option would waste time/resources getting data that is not used/useful.
WCC makes calls to autosys to also collect ALL the jobs defined to AutoSys.
Collecting an extra 10k to 30k worth of jobs or scanning for / thru them is a waste of time and resources.
The scheduler will scan thru the tables as it pulls job definitions, processes events and updates job statuses...
Typical AutoSys performance issues appear when the tables like ujo_proc_event or ujo_job_runs or ujo_machine get large, but the less you have in ujo_job_status and ujo_job could still help in general.
Monitor your "autoaggr -h" results, and as_server logs, and DBMaint.out.
Look for slow responses or statistics and trends.
If interested contact your Broadcom account team regarding an AutoSys/WCC health check?
It is something our SWAT/Services team can do, they provide you with scripts that collect data about your environment, they review it and can then give you a report on the environment.
Showing you your numbers, status, performance, recommendations, etc...