Just as FileMaker versions 7 through 11 used the same file format and file extension (.fp7). FileMaker versions 12 and 13 use the same file format and extension (.fmp12) so there is no conversion to a new file format needed.
I'm about to upgrade to 13 and wanted to know after opening 12 files in 13, will my old 12 file now be able to use all the features such as encryption as in 13 so when I save it, it technically becomes no different to a new file I created from scratch in 13?
Since the file format does not change, that should be the case, but this is all early days so we may learn more as people explore different capabilities of the new system. I do recommend caution whenever a new release comes out. Early adopters often find that there are still unresolved issues with the new release waiting to be discovered. I don't recommend that you upgrade and embark on your next major project with it just yet. Better to wait a while, experiment with the new features and watch for reports in Report an Issue before making that commitment...
As Phil said, FM 12 files can be opened by FM13 and vice versa; there is no "conversion" process.
However, be advised that any FM13 features that are added to your scripts, layouts or calculations will NOT work in FM12. For example, I have found that MOST (not all) of the new "appearance" controls (inner/outer shadows and padding) will appear properly for 12 users. But object invisibility, popovers and slide tab controls will NOT work for 12 users and will either cause extra "unknown" objects (i.e. popovers) or will be missing sections altogether (i.e. slide tab control).
on a similar note:
will I be able to edit/publish my file for Webdirect using FM12? I have a .fmp12 file hosted remotely on FMS12, but I am considering upgrading to a FMS13 server for the webdirect features. All of my workstations/clients are using FM12.
You would need FMS13 to use WebDirect. Since the file format is identical, a file created in FMP 12 should work for webDirect once you get a copy of FMS 13 installed.