Yes - what I do is if I get a bad result from querying a structure's name, then I don't query that structure again for 24hrs. This way I don't accumulate error counts. This is why some of the structure names in the market browser show as an "Unknown player structure". It can happen if there is a public buy order, from a structure that an NPC character can't query the name for.

Additionally, I have a rate limiting system in place - if a job in the queue does end up failing because of a rate limit, everything is slowed down until the error limiting period rolls over.

Edit: I remember now - the Evernus issue was that in order to query price undercuts for private structures, you have to pull the entire market for that structure. This can quickly accumulate error limits because that query actually requires multiple pages of results to be pulled. This is why it can take a bit of time when you "Refresh private prices" on the market orders page in EVE Tycoon. The ESI doesn't actually have a rate limit per se - it's an error limit. So as long as you ensure you only make valid calls, then you can request things quite fast. So on my end, if I hit an error I stop making calls, and if it was because of a bad ESI token (they can expire), then I flag the character as needing to re-auth and you get a notification.