Actually, SMT means that once core is capable of running two threads simultaneously - at the same time.
AIX sees each potential thread as a logical CPU - so when you have two processors in AIX - with SMT enabled (default) AIX schedules threads, or applicatins, spread out over 4 "cpu's".
AIX is smart enough to see that when there are only as many programs running - as there are processors - to only schedule one logical CPU per processor. So you dont lose 50% usage if you only have one application.
Cores, or processors, are built up from several smaller parts (scalar architecture). POWER5 has 9 components (if I remember correctly) and the POWER6 has two more. Simply put (I hope

), the way SMT works is: both threads want to run. If they are both using different components (mutually exclusive, or no overlap) then both instructions are executed simultaneously. Otherwise one one is run, and the other pauses. At the next cycle, the process begins again - both, or one.
In practice, this means that 30% to 60% of the time two instructions can be executed - and this gives the
system improvement figure quoted.
Getting back to original question. In very special situations SMT might slow a particular application. Personally, I have not run into in a business situation that SMT adversely affected performance, but understand that it could be an issue with scientific applications.
Basically, when in doubt, turn SMT off, and monitor. If pergormance improves - leave it off. If it gets worse, or stays the same - turn it back on.