Dariocg, That's a lot of subprojects and if all those inserted subproject result in only 300 tasks total, I have to ask, why is it not all one single project?
However, to address your issue, are you exporting a dynamic master as PDF (i.e. linked structure) or did you first convert your master to a static master for export? If you are exporting the dynamically linked master directly, I suggest you first convert to a static master (single file) and then export that. I'm guessing you'll see a significant decrease in export time.
As a quick experiment, I have a file (not a linked structure) with over 2K tasks. The PDF export took less than 2 minutes on that's with a virtual machine.