Fala,
So typically I will wash & bake a board in the lab for testing to ensure that I don't run into any complications due to leakage, but if the design is sensitive to moisture & contamination, you would have to take precautions to ensure the correct operation on a long term basis. In the short term (several hours to a day), FR4 doesn't absorb moisture fast enough that you would have to worry about re-baking the circuit very often.
For the long term, one method is to use different materials - Teflon (PTFE) for example, is sometimes used instead of FR4 for the PCB. Also, if only a few nodes are sensitive to leakage, sometimes those nodes will be connected to a teflon standoff to eliminate contact with the rest of the pcb. You can see examples of this in commercial designs such as picoammeters, sample & holds, etc...
Another technique is to use conformal coating to protect the circuit from contamination/moisture.
As far as the relays go, I guess it really depends on the particular construction. I've had problems in the past with capacitive coupling into high impedance nodes, but upon second consideration, at 1M, it may not be as much of a problem (I was working with nodes requiring a leakage of <100fA which is much higher than 1M) If you're using reed relays with short leads, then the stray capacitance is probably OK.
I'll try to dig up some references for you on all of this...