I am guessing that you have confirmed that the clicking is actually coming from the main relay because, depending on the vintage of the car there are other things that can generate clicking noises.
As MotorMouth93 notes, the ignition switch is a possible candidate. It is a bit of a back kinking exercise to get it out; but, other than that not incredibly hard to remove. Once out, it is fairly easy to pop the white cover off and examine the electrical contacts. This is mine after 20 years of use.
I removed mine to repair problems caused by a previous, badly done security system installation, not because the actual switch contacts had failed. The failure on my switch wiring could certainly cause the problems you are experiencing.
The contacts in the switch are quite robust and I expect that most switch problems are caused by dirt rather than actual contact wear. You can clean the contacts using a cotton swab with iso propyl alcohol and then apply some GB Oxgard (Home Depot, Lowes, ....) to the contacts. Oxgard is an electrically conducting grease which helps to block surface oxidation and reduces the resistance of the contact path. Do not use dielectric grease on the contacts. New switches are not (were not?) very expensive and given the inconvenience of switch R&R it is not unreasonable to just get a new one ahead of time and install it. However, given supply issues and price changes, cleaning may be a more attractive option.
It is possible that the switch is the problem; however, there are other possibilities, bad electrical connections being my favorite. When the clicking starts, what is happening on your dash? Is the voltmeter flickering at all and are the dash indicator lights flickering. I can't remember whether a brief power interruption will trigger the ECU to go through the power on test for the MIL. If the ignition switch fix does not fix the problem, I would check your + and - battery post clamps to make sure that they are clean and tight. Honda battery cable clams are notorious for being easily damaged. Also, check the electrical connections at the alternator.