The opaque server does offer better integration with Moodle. The issue is that this can not be translated to other Learning Management Systems (especially closed-source ones).
WeBWorK has a small developer community, so the focus of development activity is on features that can be used by everyone, though contributions that improve the ecosystem are always welcome.
The webworksoap service will probably be completely removed from WeBWorK at some point in the future since there are now better ways to interact with WeBWorK. One idea for replacing the opaque server would be to create a Moodle question type that uses the WeBWorK standalone renderer, though for this to happen someone would have to commit to building it.