I've seen posts on this very same NES DPCM click issue on byuu's forums when he started developing his NES emulation. The vast majority of the educated answers seem to point to sound emulation being incomplete in NES emulation in general and blargg and other audio engineering-oriented devs theorize that it was handled with the natural low-pass filtering provided by the analog components.
So first recommendation is to make sure the NES DPCM emulation is accurate; in the VGM mods of the NES players since it's someone else's code that's considerably harder, but for VGMPlay we should strive to have the most accurate sound emulation possible (maybe even that of the recently resurrected Nestopia; check
this TASVideos page for NES accuracy test results). The linked test results page says Nintendulator has the most accurate APU and it's
open-source so maybe consider that? Second thing is that if the issue isn't in our choice of NES APU core, then we should probably add a toggle for some basic filtering or something for certain chips.
Last resort is to force changing of the command, since this one in particular is a destructive action that also has the potential to completely change the resulting output. Maybe have the console output a warning when someone runs this command telling them it's destructive, possibly allowing removal of the warning via config file editing?