I try and maintain the 1" node spacing right from the start. Once I've got my light set I keep raising it as the plants grow. After the stop their vertical growth, usually around the end of week 6, I then lower it for flowering.
I don't think the air from the humidifier will hurt the plants, although I have to say I have never used one, so am not 100% certain. 40% isn't bad and will be about where you want it later in flower. Too much humidity when the buds get thick can cause mold and/or mildew. During my last grow my humidity was staying between 50 and 60% and I got some mold on my buds. Unfortunately I don't have room for a dehumidifier, so added another fan for better circulation.
Don't forget, your exhaust fan is removing some of the humidity, which may explain why you can't get it any higher.