I know it's not a good idea to short-circuit a charged capacitor, especially a large electrolytic. What about smaller caps - like a low voltage ceramic disc of 0.1uF or less? And if the shorting element is a low-power switch like one of those ubiquitous little square tactile microswitches, is the discharge energy enough to erode the contacts and shorten its life significantly?
If it helps evaluate the situation, take as an example two cross-coupled NAND gates in the classic toggle switch configuration. As a bias to determine the initial state, say one input of one NAND element has the small cap to ground and is tied to Vdd via a resistor of ~100k. The microswitch parallels the capacitor. Is it advisable to insert a series resistor to limit the discharge current?