I am a major proponent of bicycle patches. I patch tubes as often as necessary on all of my folding bikes. I have four patches on my current tube. I believe patching is better for the environment, cheaper and easier to carry on the road ( due to small size ).
I never saw any side effects from patching. This week I found one. I was at a shop two weeks ago and the tech used a compressor to inflate my rear tire. He overinflated it, a few days later I got a flat. A patch failed and I had to repatch. Two weeks later, two more patches failed. One had a hemorrhage at a point and the air eventually leaked out the other end. While the second was a catastrophic failure just above the rip in the tube.
Overall, I am still a proponent of patching, however it is important not to overinflate with a compressor.