I asked a NamUs rep about adding names to the lists. This is my understanding of how it works, based on my interactions with them. It may have changed since then.
At the time, they told me that updating the list is a manual process. But they said they don't put names/cases on the rule out lists that were ruled out automatically by CODIS. They said if both have DNA in CODIS, and they're not on the rule out list, to assume they have been compare, even if not listed. The problem is we can't see who's holding the DNA, or who has DNA anymore. They only update it when there's been a manual comparison to make the rule outs. They do this because the automatic ruleouts would be in the hundreds, possibly thousands, if they had to list each and every one a set of remains was compared to. And someone would have to go in and add it. Twice. One on the MP side, one on the UP side. For each exclusion. That's how it sounded to me when they explained it.
I think they make exceptions, though, for example, like when they're bombarded with suggestions for the same MP over and over for a UP. I also know they made a couple of exceptions for adding Canadian missing people to a UP's list, which they normally don't do. When Patricia Salamandyk was ruled out for Buckskin Girl, Marcia King, they listed her in the rule outs, even though she was from Canada. I think they did that because of the preponderance of suggestions for them to be a match.