Automatically hide latex aux files in finder (files with a certain extension)
Hiding all files isn’t implemented on a system level: make a certain file type hidden

Hiding files one by one is trivial:

 chflags hidden /path/to/*\.aux


I haven't seen a way to implement all the logic required to do what you ask, but I have seen people make up smart folders to show only specific files in a folder that match the good extensions. If your list of places where you want to filter is small, that effort will be less than scripting the hide tool you need. 

Have you ruled out configuring latex to put all auxiliary files in a hidden subdirectory/folder that you name with a dot like .tmp? This is shown here for pdflatex -output-directory=\.tmp

Alternatively, you could use a make tool like rubber or latexmk to either run your custom hide script or even discard those files when you compile successfully. You’d only then need to mark in some way what folders get the hidden treatment.