Not possible right now, sorry.
It has been suggested before: http://talk.dynalist.io/t/option-to-exclude-document-from-global-search/544
The main issue is that since we don't want you to do "exclude:[super long file id]", files need aliases to be useful. That would involve a new alias system, which is not really necessary at the point.
Maybe there are other ways you imagine we can implement this without aliases?