At least with Reaper, if you cut an audio clip it will, by default, automatically apply small adjustable fade in/out envelopes to the ends so you specifically don't have to manually do it.

Yeah, every software/hardware seems to deal with this differently. The sampler I use the most (Octatrack) only jumps by zero-crossings when holding SHIFT, otherwise lets you freely create entirely new pops and cracks in your songs :)