In practice the system speed of modern desktop systems is not the key limiter of timer frequency.
Timers can be implemented by interrupt, by sleeping, or by polling.
For interrupts, the program (MATLAB itself) would request that an interrupt routine be called at a particular [usually relative] time. The limit in such cases is on the time taken to take a hardware interrupt and do a context switch. The time required on MS Windows systems to interrupt and context switch has been more or less unchanged since the days of NT4, and stands at about 50 microseconds (or less if context switches are not necessary.) 50 microseconds is a few orders of magnitude faster than Sridhar is seeing, so we can deduce that MATLAB is not using this mechanism.
sleeping is putting in an operating system request to be re-awoken at a particular [relative] time. The POSIX standard on this facility is a based upon a clock rate minimum of 60 clicks (ticks per second), with some OS going to 100, but hardly anyone going past that. Windows Media Timers occur at 64 Hz which is right in line with this, suggesting that the Windows Media Timers might be based upon this kind of timer.
Polling is an arrangement in which the software executes in a loop, checking the time at the top of the loop and executing any timers that have expired (that is, need to be fired), and then after those, going on to the regular work. There are aspects of how MATLAB handles timer interrupts that are consistent with this mechanism.
But what is actually used by interpreters such as MATLAB? It can be a mix. There might well be an interrupt timer fired by hardware, but usually the interrupt routine just sets a flag indicating that some timer has expired; when the interpreter loop hits that point in the cycle and finds the flag set, it services its interrupt queue. Why not just read the precision system timer each loop? Because reading the precision system time is a relatively slow operation, especially if you use an official operating system call instead of running with elevated privileges and reading the hardware timers at the program level. Checking a flag is fast.
Interpreters do not usually service extended interrupts through a direct hardware interrupt routine because interpreters usually have too much complex state to risk doing that.
Windows offers a High Precision Event Timer (HPET), which is a count-up device running at a minimum of 10 megahertz, and which goes off when the count matches the target time. I have found no evidence that MATLAB uses this timer for anything.
You may wish to examine this blog article which describes how MATLAB uses Windows cycle counters to measure elapsed time between events. Measuring elapsed time between events is a notably different activity than relative time timers or (especially) absolute time timers. 
