With T101648 (June 2015) per-filter profiling was removed because it was slowing down the saving of edits. @dmaza did some fantastic investigation and it looks like since that time, the code was reworked so that the profiling happened after the edit was saved. This hopefully means we are safe to re-enable the profiling on wikis where it was removed, as this feature was hugely helpful and is sorely missed.
Relevant commit that deferred the profiling to after the edit was saved: rEABF43a538fe (April 2016)
We now have a Grafana dashboard showing overall AbuseFilter runtimes, so we could perhaps use that to see if the per-filter profiling is slowing anything down. I thought the Portuguese Wikipedia would be a good one to start with, as it has a lot a filters and is big enough to provide meaningful data, but is not quite as risky as enwiki.