If I recall correctly DQMH Main VIs still pop up for us (on PharLap Systems with LV2020 32bits SP1). We don't deploy as often as we used to; now we're mostly running on compiled .rtexe without GUI.
For generic sub-VIs, unchecking "Clear indicators when called" as indicated above worked nicely for us.
NI may be working to fix this issue, but I don't expect they'll fix it for older LabVIEW versions or PharLap.
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Although I've been 10+ years long fan of LabVIEW, I started to discourage engineers to start new projects in a
SaaS language. NI must first regain trust within its community.