In my experience, over 20 years on big bastard things costing millions of $ all the way down to laptops...
Having a single logical CPU causes a lot more bother, as you can't interrupt a wayward process/thread easily to kill it, or dump the OS if it does it in privileged code or an interrupt handler.
Windows programs are often retarded and try to handle the screen and other stuff in the same thread, but anything properly written will be threaded.
Multithreading/multiprocessing is something software designers struggled with for a long time in the windows world. I've lost track of the number of dumps I've looked through caused by badly written anti-virus filter drivers over the last 5 years in windows. It seems they are over the hump of this now and get some of the principles involved.
Now that there are 'effectively free' multiprocessor systems available, I'd strongly recommend you don't go for anything less than a core 2 duo based system.