How will NMOS Vt be effected if the bulk and source is not at GND but at higher positive potential due to isolated pwell leaking to deep nwell
The body effect is the normal mechanism that will affect the threshold voltage. If the body is biased above the source (for NMOS), the threshold voltage will decrease by an amount approximately equal to the bias.

If the source and bulk are connected, I would not expect to see a change in the threshold. However, the VGS voltage could be effectively reduced if the gate voltage is generated with respect to ground.

In any case, it seems like going heavy on body contacts is a good way to combat this problem.