May I ask how this makes your windows os non-genuine or pirated version?

I get that technically motherboard upgrade makes it a new pc, and if you had bought your original key in the OEM channel, then it would require new key.

But if you just call Microsoft’s activation support, they will transfer that activation to the new motherboard.

So how is that new computer in any greater risk of malware or viruses getting in to it than pc that has been activated using retail key.

Those illegal windows activators however are different story, as you really don’t know how they do their activation bypass hacks.
They can claim to do just that activation, but there is still a risk of that they leave backdoors to attackers to exploit.
But long as you stay away from those activators and have bought your key from legitimate seller/store, I cannot see any greater risk of doing that motherboard upgrade with same key.