The problem was indeed related to the <exclude>*.xml</exclude>
as suggested by @cowls.
But the root cause was due to the fact that when there's at least one <resource>
element then the default filtering behavior doesn't apply anymore.
The default filtering behavior is to includer resources under src/main/resources in the build, without filtering. So without that default behavior, the beans.xml which was under src/main/resources wasn't included in the build, thus CDI stopped working.
In order to fix this issue, a 'default' resource had to be included:
<resource>
<directory>src/main/resources</directory>
</resource>
More information can be found here.