Hi,
unfortunately, Java files greater than 10k that are not generated are sometimes found in legacy Java projects even if it's a bad practice.
I've seen that with SonarLint for Eclipse, huge Java files don't cause Eclipse to lag that much if Eclipse has enough memory.
However, SonarLint for IntelliJ lags more with these files then Eclipse after one of them is opened (the editor can stop to be responsive for a good amount of time). If a Java project has one or many of these huge Java files, the solution is to disable the automatic trigger of analysis. If the IDE has big performance issue when huge files are opened (not even edited), many developers will prefer to run SonarLint manually. But IntelliJ without SonarLint already has trouble with huge Java files, so it's not like SonarLint is the only cause of the lag.
Huge Java files could also be a reason why someone would try to use sonar.exclusions to force the exclusions of some huge Java classes that are part of the source folders.