Can I modify woocommerce themes that are under the GNU General Public License, version 2

Under the license it says:

"Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed."

This is talking about the license itself. You can't take a GPL theme, modify it then announce it's under the OMGWTFBBQ license. It has to remain GPL, hence the term copyleft license

Does that mean I can't modify the source code(template files, css, html etc), even if I'm using it as a template for my store and not reselling it or anything like that?

If it's in the privacy of your own server, undistributed, then sure do whatever you want to it.

If you plan to distribute it, that's ok too, as long as it remains GPL. You can even sell it if you want, but that would be a pretty shady move ( but a legal move ), as long as you comply with the GPL license you're fine

Note that I and others can't say very much more on the subject as we're fast moving into the realms of legality, and non-WP specifics. If you want further details on what you can and can't do, you're going to have to get a professional legal opinion