Something I've wondered too, but never bothered to actually check until I read your post. As far as I can tell, Max evaluates aliases it encounters in the search path just as if the aliased file or folder was actually within the Max search path.
For some reason the forums aren't letting me edit my previous message, just thought I'd add that I tested this on Max/MSP 4.6.3 on OSX 10.4.11. Don't know if the windows version will behave the same, hope so :)
Several years ago I documented the circumstances in which Max resolved HFS aliases and in which it did not resolve aliases. A quick Google only turns up a different message in which I complained that the Extras menu doesn't resolve aliases.
Of the top of my head: aliases to folders in the Search Path are resolved and added to the Search Path. That's about all. Aliases to objects are not resolved, folder aliases in Extras|Clippings|Inspectors are not resolved, aliases to startup items are not resolved. Etc.
I still find it very frustrating that Max is inconsistent in its handling of Aliases, but I suppose we should be grateful for what we get.-(
You may want to read DDZ's response to the issue at . That will also give you a hint about the Windows side of your question.