Harmfull for root system to have some oxygen through drainage holes???

Have somewhat of a problem here.........im almost about to start going into week 6 of flowering and my roots have outgrown the 5 gallon buckets of soil that they sit in. The roots grew through the drainage holes in the bottom of the bucket. However, the bucket sits inside another 5 gallon bucket so that there is a little drainage reservoir that can hold a few inches of runoff water. The roots were just laying in the runoff water for god knows how long, causing my plant to yellow up and spot.......i did not even know this was going on until i seperated the buckets and saw all the roots sitting in the runoff water..........i flushed, drained the reservoir completely and redrilled a drainage hole in the reservoir at the bottom so that no excess runoff water could build up again.........my question is that if some of my plant's roots are just sitting in that extra reservoir, do they need to be in water at some point so they dont dry out, or will they like to soak up the oxygen and use the rest of its root system in the bucket to pull in its nutrients....???the pics of the the roots through the drainage holes are in the post by me just before this one.......check it out and let me know what you think.......