Network Atlas variables not updating anymore after sp4 update

This is a known defect, issue #14072 for anyone interested

When will that be rectified ? SP5 ?

I can say for sure not SP5, SP5 was released a few weeks back and is only required if you have IPAM 1.5, so no need to upgrade to it.  Beyond that I cannot say for sure right now

is there any ETA on when this issue will be resolved? It is fairly important to us that this is fixed.

This should be addressed with 10.0 which just went GA.  Check your customer portal to see if the bits are there, we are in the middle of provisioning now so if they are not, you can call support to get the direct link, PM me via thwack to get the direct link or wait a few more hours and check back.