Can you provide little more information regarding this setup also if i'm correct vCenter is deployed in Singapore DC ?

1. What if you deploy all three VM's in Hongkong DC ? Are they communicating like how they communicated earlier in Singapore DC ?

2.What sort of communication failure are you facing ?

3. What type of network is connected to DLR uplink ? VXLAN,VLAN ?

Also remember Since you have only ESXI host in each cluster . The only phase where VM's demand to connect/communicate via physical network is when you place them in two sites(Two Hosts in your case managed by one vc)

If i'm not wrong your problem is only  Host VLAN's are stretched in this set-up .

You mention vDC, are you using vCloud Director?

Do the VMs deployed on VXLANs or VLANs?
You would need to draw or explain how do you setup the VM networking e.g. VXLAN/VLAN that being used by VMs, if any NSX DLR and/or NSX Edge, how do the connectivity look like.

Is the VXLANs stretched across cluster?

If you are using VXLAN and you want stretched VXLAN across Singapore - Hongkong, you would need the MTU to be minimum 1600 across them, including WAN if the clusters are connected across WAN.

To test VXLAN, you can do a logical switch ping from Networking & Security > Logical Switch > Logical Switch name > Monitor > Ping / Broadcast

You can also check VTEP to VTEP ping using vmkping command as below:

    vmkping ++netstack=vxlan <vmknic IP> -d -s <packet size>

See this KB: Testing VMkernel network connectivity with the vmkping command (1003728) | VMware KB

Main question is about running ESXi hosts with two different VLAN's one for NSX Management and other for Computer cluster > which VLAN are you referring to?

ESXi management VLAN?

VXLAN Transport/VTEP VLAN?

or something else?

Do you have any logical network diagram how the VDC singapore connected to VDC hongkong?

I assume they are on different site

MTU 1600: if it's a stretched VXLAN - same Logical Switch spanning across cluster in Singapore and cluster in Hongkong then yes you need MTU 1600 end to end.

You mentioned that DLR has Transit Network Uplink and three Internal VXLAN's.

Is the DLR shared across cluster in Singapore and cluster in Hongkong?

You mentioned there are three internal VXLAN Logical Switches. Are the three internal VXLANs shared between cluster in Singapore and cluster in Hongkong? three for both or three for each so total six?

For multi-site deployment, you can review the options and requirements based on NSX-V Multi-site Options and Cross-VC NSX Design Guide

As per table below taken from the guide, NSX with separate clusters require MTU 1600

Appreciate that update .If possible place two VM's on same Logical switch and ensure they are running on two hosts(in your case hosts in two sites) . I want to see Overlay connectivity results between two sites before checking/confirming DLR and routing side of the config.