I think it really depends on how the system is setup for transmitting and receiving. My impression is that most of the repeaters for Boulder County are activated only when it receives the correct tone squelch in order to limit interference from things like skip. This would mean that all radios are programmed to transmit using only the correct tone squelches if they are used for repeater operations.
The other way of handling repeaters is to have a carrier signal activated repeater, which would allow for any radio on that frequency to transmit regardless of tone squelch. Like noted in the above, this would allow for interference to activate the repeater at any given time and is a less likely configuration for repeater use.
I've drawn this conclusion from the previously mentioned fact that I have been scanning Boulder County without any tone squelches and have not noticed any transmissions, sans repeater CWIDs that use carrier squelch only, that have used a different tone as the ones listed in the database. The only difference I have experienced between using one and not using one is that my scanner seems to open up a little faster than with a tone squelch and may hold onto very weak signals a little longer, otherwise it doesn't really change much. I generally favor not monitoring with a tone squelch unless I run into considerable interference from another user on the same frequency (not likely in Colorado). If you don't like your radio locking on a frequency because the repeater is identifying itself, then using the tone squelch is not a bad idea.