Regarding the VHDX per LUN or not, I'd personally go with more LUNs on the A90. ONTAP thrives with more parallel access; more FlexVols.
ONTAP 9.15.1 (which you'd have to at least be on to support an A90) does have some improvements to increase resources available to single FlexVols, but more volumes and spreading the load is typically more performant.
I always start with at least 8 FlexVols, 4 per controller, and then a LUN per volume (thats on smaller A250 systems, for example).
For an A90 I'd go 8 or 12 volumes per-controller initially as ONTAP loves those CPU cores. How you want to distribute your VHDX's across those LUNs is up to you. But if you have VMs that hit all their disks at the same time, maybe try and spread those VHDX's across multiple volumes and both controllers.