One of my datafiles are growing into 10K lines. It's used on command (CUI), so not called that often. But when it's used, it may cause stuttering? 
Certain users have a few hundred entries. 

https://umod.org/documentation/umod/api/data-files#using-a-data-file

I think you may rework your plugin or ask it's developer to add an ability to work with MySql/Sqlite? That might be faster, at least depends on the content, amount of entries, .

good point. does structure of the data matter much or is it mostly the size of the whole file?

Data structure is important. There may be 10 entries with 100 lines, or 1000 entries with 1 lineS in each. Secondwould be much more slower.