I've used USAJobs to apply for multiple positions and, having also worked in VA and been involved in hiring to a small extent, can say it is very much a functioning job site. The issue is that depending on the VA, HR usually receives and screens the applications first before ever sending them along to the particular service (e.g., Mental Health) that posted the ad. Thus, HR may screen out applications because, in their minds, a candidate does not meet requirements when, if the service had seen the application, it would be clear the applicant is qualified. HR may also screen out applications that they deem to be incomplete for whatever reason. And there can also be significant lag times between when a site receives an application and when they communicate with applicants/setup interviews; for example, I've heard of folks being contacted 6 months after applying. There's often an email address listed in the job postings (sometimes an HR person and sometimes not), and it can be worthwhile emailing that person to see if materials have been received, where they are in the process, etc. I'd probably wait at least a few weeks after applying before doing so, though.
Also, if the positions in HI are very high-demand, it's possible they have multiple internal candidates (from HI or other VAs) who are also applying, and so the positions may never necessary get past that point.