There is nothing that ties JSR-299 to Servlet, it can operate in an EJB environment for example.
I think web-beans.xml (or beans.xml now) has more in common with components.xml from Seam than with seam.properties...
Manually registering modules in a central metadata file is an anti-pattern that causes all kinds of problems for tooling and frameworks. A module should be able to register itself.
Empty xml files could give issues with some build systems requiring well formed or valid xml files.
Fortunately web beans supports non-empty beans.xml files :)
(In contrast empty properties file are valid properties files)