> it all comes to NETAPP or ESXi iSCSI implementation (but switching to iSCSI HBA NIC does not change anything), so I believe it's Netapp fault.
Interesting.
> I checked Initiator group settings, it's LINUX. VMFS partition alignment is ok (starting sector 2048, but it's weird, according to ONTAP manual it should be 0),
Partition alignment recommendations for various OS can be found here.
https://kb.netapp.com/onprem/ontap/da/SAN/How_to_identify_unaligned_IO_on_LUNs
For ESXi, I'd try 0 as suggested.
For Windows partitions on ESXi VMDKs, I'd try alignment recommendations for Windows.
Using ESXi CLI partitioning tool (although you probably wouldn't need it to start at 0):
https://kb.vmware.com/s/article/1036609
As always, don't try new stuff on production LUNs or datastores!