Its depends from your code (single-loop application or multiple loops, executed parallel), computer (single processor or multiple processors), etc. Normaly performance changed depends from this setting, but not always....
There are a lot of articles which can be found on the NI web site:
Using LabVIEW to Create Multithreaded Applications for Maximum Performance and Reliability
http://zone.ni.com/devzone/conceptd.nsf/webmain/D2E196C7416F373A862568690074C759?opendocument&node=dz00000_us
LabVIEW and Hyperthreading
http://zone.ni.com/devzone/conceptd.nsf/webmain/01F2E634710FB8E486256E2900586D41?opendocument&node=dz00000_us
Why Would I Want to Turn Off Multithreading?
http://digital.ni.com/public.nsf/3efedde4322fef19862567740067f3cc/87d02b
a4155a0076862565bc006c2dd7?OpenDocument
If I Use Multithreading, Will My Application Run Faster?
http://digital.ni.com/public.nsf/3efedde4322fef19862567740067f3cc/bcc1864c520e1814862565bc006b1b18?OpenDocument