Fix visibility reference check
What does this MR do?
When all references in a system note are checked, it's not reliable to check if there was any not-visible reference returned by an individual parser because that reference could be satisfied by another parser.
For example if @jprovaznik is referenced in a commit message, then it wouldn't be recognized as a visible reference by group reference filter (because it's a user), but it will be recognized by user reference filter. So although some filters may return "invisible" nodes, as long as all nodes are marked as visible by a filter, the note should be still visible.
Instead we check if in the end all nodes were visible.
Related to #336491 (closed)
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How to setup and validate locally (strongly suggested)
Does this MR meet the acceptance criteria?
Conformity
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