VMware vSphere

I have a customer or builds clusters that have some hosts with HT enabled and others without. 

I have always followed best practices in keeping the hosts identical in settings but the customer mentions that there is nothing in the Best Practices guide that says changing the HT setting on a single host is against best practice. 

My thoughts would be that It could potentially create performance disparity in the event that VM's are on different hosts.

I am looking for thoughts on this.....

Cheers,

That's correct, it could (and will) create a performance disparity. What type and how severe, though, depends on the workload and also the level of contention plus the version of ESXi. The best practice is always to configure hosts identically intra cluster and to use the same hardware for all hosts.