It's not clear to me what the behavior should be, given that Org mode itself seems confusing when exporting cross references to HTML.

For instance, Org will substitute links to internal references with a counter for most elements, but with \eqref for equations. We shouldn't do that since it's dependent on export. The Id of InternalTarget should be used for \eqref or something else on export. Still proper numbering for equations is too complicated. For other elements you can reference anything with #+name but this counter is only updated in the presence of #+caption. I will have to figure out how numbering for <<targets>> works.