CO2 will lower the pH in your tank. This is how a controller works. You set a pH level and when it goes above that, it turns on the CO2, and when it drops below it turns it off. Of course you have to set it below your aquarium's natural point. You can adjust the buffering capacity of the water and add a little baking soda to push it to turn on the CO2.
Without a controller, people often turn off the CO2 at night because without light, the plants don't photosynthesize. However my tank with the controller will turn it on even with the lights off since it's going by pH. In theory leaving it on all night could negatively affect your pH, causing it to drop since it isn't being consumed. But at the low level you must be using to run it all the time, it probably wouldn't be a problem either way. The main thing is to monitor your reactor... if you see a large bubble forming, you should turn it down.
I run my main regulator at about 20psi and use a needle valve to lower it to 1-2 bubbles per second. As the pressure in the tank decreases, I have to open the main valve more to get it back to 20psi or so. I do have a splitter and second needle valve going to a second tank. I split it before the solenoid so it runs all the time at a slower rate. I use Tom Barr's homemade reactor design in that tank and it works quite well. The 150 gallon tank with the controller has a big reactor with bio-balls in it. I'm not sure what I will use in my new tanks.
Michael