When using WP Empire Builder, will I be able to upgrade my Wordpress version when a new one becomes available?
Yes you should. WP Empire Builder doesn't interfere with that process at any point. If you are unable to upgrade, there can be several other reasons why.
For example, maybe you unintentionally modified some files manually, or another plugin did this, or even the host uses a modified WordPress package in their Fanatstico installation.
If for some reason you aren't able to upgrade, please first contact your host about it.