You should be fine.
Was there like a periodical decline (daily or weekly) in the performance in running it continuously that long? Usually, I experience some slowness after a day or two of just keeping the computer on. But that's of course just a regular computer setup. If I may ask, what's your setup for your mining rig?
From my experience I do not see any performance degradation at all after running mining rigs for months on end. I periodically choose to shut down for cleaning as stated earlier, but most of my rigs do not crash, hang, reboot, or lose any mining performance whatsoever. I have rigs running under both Windows and Linux and can make the same claim for both.
The key is to create a solid working environment, meaning quality hardware and risers, a stable OS install, proper settings, stable drivers, and tweaking your GPUs to run optimally. This does not mean run everything balls to the wall trying to eek out every last hash, as then you will probably run into many issues. I try to optimize my rigs to get a good hash-rate versus lower power consumption while still being stable.
If the settings I choose make a rig unstable where it cannot run a solid week without running into problems, such as hangs or reboots, than I know I was too aggressive in something and will back down the clocks or up the voltage sightly to stabilize it. If after this it is still ustable I will look into other factors, such as drivers, PSU, are the connections tight, etc., until I can get the rig stable.
After building quite a few I know what works and what doesn't so it is easier now than it was at first, but the main point of all this is that a mining rig is very capable of running very solidly for long periods of time (months), without user intervention. If your rig is having trouble and routinely hangs or reboots, you are missing something in its build or configuration. You might want to back off on timings a bit to start. I can assure you that 1 or 2 Mhash/sec loss per rig will be more than offset over the long run by the continuous run-time of weeks or months on end versus having to reboot or restart a hanged rig every few days that may run slightly faster.