This scenario, saving a scene with a missing plugin, is generally pretty obscure in all software that supports 3rd party "plugins".
I have never seen any documentation mention anything about it, much less announce it as an official feature.
Still, it seems to be silently supported by Maya and 3ds Max (don't know about others). But "silent" and "unofficial" often means that it's not guaranteed to work.
In general, support for this feature isn't in the hands of the plugin author, because, well, when the scene is saved the plugin code is completely missing. It is up to the host system to preserve all plugin data that was loaded in absence of the plugin.
The only control the plugin author has in this situation is simply to follow the guidelines of the host SDK about saving data into the scene.
That's what Ornatrix does on all hosts, 3ds Max, Maya and C4D. In 3ds Max this scenario works at 100% (can't speak about C4D, I think we haven't tested it explicitly, but we also haven't had any complaints about it so far).
In the case of Maya, we keep all Ornatrix data using the official ways, in attributes of built-in types and of our MPxData-derived types that support serialization to both ASCII and binary scenes.
And saving without Ornatrix seems to work, however, we had a report recently that ramps were not preserved. More investigation showed that any "compound" attributes get broken when saved with a missing plugin, for some reason Maya saves just the first child attribute of the compound. Maya's own Ramp attribute is implemented as an array of compound attributes, so all of our ramp attributes get broken when saved without the plugin. We also keep a couple other attributes as compounds, partings in HairFromGuides and slopeRampOverrideData in SurfaceComb. So these two will also break on "save without Ox".
I can see two ways to approach this problem in Maya. First, complain to Autodesk about it. You say that the "majority" of other plugins support this feature, have you noticed any that don't, besides Ornatrix? I expect that any plugin using compound attributes will be one of them. So if you want, you may report the problem to Autodesk yourself. We may do it too on our side.
The other way is to work around the problem, which means to change all compound attributes in Ornatrix to something else. But this would be a lot of work and trouble (complicating the code to load the obsolete compound attribtutes and converting them to their new types) that we would very much prefer to avoid.
You also mention that you've experienced broken connections when loading such scenes. I haven't noticed this in my tests, so if you have a 100% reproducible example scene, please send it to us. But again, if there is a problem with connections too, I don't see what we could do about it, given that Ornatrix can't be responsible in any way for maintaining the connections when not being loaded at all.
Ivan Kolev (Software Developer, EPHERE Inc.)
E-mail: ivan.kolev at ephere dot com
Discord: ikolev