The answer to all your questions is yes:
- you can store pdfs or other files either in Content Builder or in your sFTP
- you can use AMPscript to attach the files to your emails
- you can use AMPscript to dynamically match subscriber data with files and to create conditional statements
- you can match a file based on a filename, customer key, etc.
Some examples can be found in the ampscript.guide: https://ampscript.guide/attachfile/