The limit is because instead of giving each thing to ignore it's own entry in the INI, we try to put them all in one INI entry. Which means that there is a maximum of 2048 characters that can be on the list, including the pipes.
spawn names max at 64 characters, so we'll assume 65 for each spawn to include the pipe. So that means at a minimum you can add 31 spawns to the list. But you'd be hard pressed to find 31 mobs with exactly 64 character long name. In fact, you'd be hard pressed to find 1 or 2 tbh.
With that said, it's more likely to find spawns with 20 characters and under in their name which means you'd be able to add 100+ spawns to the list in theory. If you're in a position that you need to ignore around 100 spawns by name then it's highly recommended you find alternate ways to exclude them, or as Sic suggested, use the right tool for the job.
The plugins use alert list 1 to ignore things based on spawnsearch. Which means you can rule out entire races if that fits the bill.
Here's the information on alerts.
and here is the information on options for Spawn searching.
You can add things to alert 1, to ignore them. The alerts are temporary. Pretty sure they clear when you zone, but at a minimum reset when you close the game and come back.
But again, right tool for the right job. You can use a rake to clear out snow, but you'd be better served with a snow blower. Tools like pocketfarm.mac, MQ2Farmtest etc all have their place and their designed purpose. The plugins are meant to engage with content and work as a group to defeat the content. If you're fighting things that are not a challenge, or you're simply plowing through them without hardly a moment between kills, then they are definitely not optimized for that sort of combat. Simply doing away with a pull ability can increase your kill count by over double or triple for example. Since you're not going to them, hitting them with an ability, waiting for them to arrive etc. You just run up and slap them in the mouth and it's usually 1 or 2 hits to kill them, then you turn to the next one.