Normally I would say 25,000 files isn't that much for tagging but I've never tried a ton of HTML with embedded PHP. You say you are currently tagging all the files. Did you use the Tag Files dialog? If so, I recommend you remove that tag file, create a workspace/project, and add files files to the project. There won't be a difference in symbol analysis but it will be much easier to open files in the workspace. You use the command line so "e name-without-path" will kick but.
Here's another tip. Use "sgrep" in the Build window since next-error, prev-error, and cursor-error work (sgrep <something> -t "*.php").
The good news is that namespace support for PHP will take a high priority. Right now, it doesn't look like we can add it until v20.
I assume the .html vs .phpscript you are seeing is because you brought up Project Properties and you don't have a project open. It should always show .html for a .php file unless you manually changed the mode and it got saved away. Can you reproduce this (.phpscript shown) with a default config by just editing a particular file? Start SlickEdit with "vs -sc some-directory-which-does-not-exists" for a default config.