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The hole is a weep hole, designed to drain coolant from water pump seal leakage or oil from bearing seal leakage from contaminating either system. So one of the seals is leaking, and you should rebuild the pump.
Looking at the parts diagram it appears the impeller is threaded onto the shaft on the YZ250....hope that helps, heres the parts diagram http://www.mrcycles.com/fiche_section_detail.asp?section=50188&category=Motorcycles&make=YAMAHA&year=2004&fveh=1236
your water pump shaft runs threw bearing and seal,and your seal is bad,not to big of job to replace,you can order part off bike-bandit.com( they also have a breakdown of parts picture you can look at to help in seeing what needs to be removed to fix) and it will be ok to ride as long as you do not let the colant run out( no colant =overheat=locked up engine.) so check colant every 5-min of riding untill you fix.....
leaking water means the seal is gone, the bearing is in the clutch case, often needs a new shaft as well if it has wear marks, replace the bearing, it will help the new seal last longer
Water coming out of the hole is to indicate that the pump seals need to be replaced. Some water is probably in the gearbox now. If the oil is whiteish you do. Pull the right case cover then remove the pump cover and the impeller then replace the seals. Remove the liquid gasket so that the hole is open again. You can see a parts diagram at www.babbittsonline.com Click on the red "OEM PARTS" tab. Items 6 and 7 are the seals separating the water from the oil. Put a wrench on the impeller shaft next to the gear, then unscrew the impeller as if it were a screw. It would be good to replace the gasket (item 10) as well. Please take a moment and rate my answer to your problem.
if it is just a small hole you can use a steel epoxy on it but you must polished round portion of the hole your going to sealed. but the best is buy new one.
its the water pump tell tale hole. if it is leaking it needs new water pump seal its pretty cheap and easy to fix also check the shaft isnt worn when you have it apart.
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