Apparently System-scope custom fields have a significant performance hit in Jira. I think project-scope custom fields are better.
Sometimes it feels like Jira is so incredibly configurable but is really missing the "pit of success". There is a way to make it nice to use and reasonably performant, but you really need to go into it with a strong plan. And even then it's really easy to balls it all up in short order if you're not vigilant.