My floor joists do have pre-cut knockouts - however the joists are not all lined up so the holes vary. I need to run a few lines perpendicular to my joists. I am thinking about drilling holes near each other 1/4" larger than my pex to run my lines. The alternative is to install them just below the joists. I am unsure of my future basement ceiling. Is it worth fighting the holes and trying to get holes drilled in a straight path for the pex to snake through or better to just clip it on the bottom of the joists?
Just line up the holes and run the line. You are thinking about this too much. The last thing you want to do is put these below the joists.
if you have people in your basement this would make it really easy to just reach up and hang on or whatever.
if you move these in the future it will assuredly be harder - and why set yourself up to move something.
the PEX could even get in the way of a drop ceiling.
the PEX is more secure in the joists
You said "I am unsure of my future basement ceiling."
If that is the case you may want to put them up in the joists in case usually want to out in a hard ceiling (something I would recommend against).
Otherwise just run them on the bottom of the joists and plan on a drop ceiling if you want one later.