What I meant by “slow” down is that the scheduling cycle would take longer since you have more jobs to consider in a scheduling cycle.
Another thing that you could do is to set up a routing queue and an execution queue. Then you could limit the number of jobs in the execution queue on a per user basis to a 100-500 hundred. This will help the scheduler since it only looks at the jobs in the execution queue. This way you can submit all of the jobs needed an PBS would route them to the execution queue as needed.
The other option it to build PBS using the master branch test that out. The next release for PBS Pro 18.1 is targeted for the end of March 2018.