Sorry but I think you're wrong: the battery supplies the CMOS terminals. If you don't interrupt that supply before shorting the CMOS terminals, you'll be also shorting the battery's terminals, and therefore reducing its life.
And the instructions for clearing the CMOS values on my motherboard's manual agree with me: turn off PC; remove battery; wait 1 minute or short the CLEAR CMOS pins for 5 seconds; reinsert the battery; turn the PC back on.
The manual even says that you can "use a metal object like a screwdriver to touch the positive and negative terminals of the battery holder, making them short for 5 seconds."
So, shorting the CLEAR CMOS pins is the same as shorting the battery holder, which will obviously short the battery as well if it hasn't been previously removed, like the manual says...
And besides from reducing the battery's life, it's also not a good idea to try to clear the CMOS without removing the battery first because on one hand you want to the voltage on the CMOS terminals to be zero, but on the other hand the battery will still be trying to supply 3 V to the CMOS terminals, generating a high current, and whether or not the voltage at the CMOS terminals drops to zero will depend on the relative resistances of the short you make with the screwdriver, the resistance of the path between the battery and the CMOS terminals, and the internal resistance of the battery.
So also in order to ensure a good clearing of the CMOS values, you will want to remove the battery first, otherwise some of its current may leak to the CMOS (if the voltage at its terminals is not exactly zero) and it may keep its values, unless you short the CMOS terminals for a very long time, but then you'll definitely end with a complete discharged CMOS battery.