Hi @salias ,
I would go with your option 2 (removing poorly classified sequences) after checking a few with NCBI BLAST to see what else they may hit.
Most ITS primers can amplify non-fungal eukaryotes, and if these are not represented in your database you will often get these poor classifications. So it is often a good idea to use the UNITE fungi +_eukaryote database to detect these non-target hits.
Presumably you don't want non-fungi in your survey, so I would just remove them (after confirming that they are non-fungal or junk etc)
This might not be a good idea either, as you might then still include these in alpha and beta diversity and other measurements where having non-target sequences present could lead to misleading results. But that depends on your biological question and methods...