I was watching It's Only A Paper Moon yesterday (the episode where Nog lives in the Vic Fontaine holosuite programme while working through his PTSD) and it made me wonder:

Where was the bathroom? He was there for several weeks without leaving so where did he go to answer the 'call of doody'?

I would assume he just used the bathroom in the holographic building. Afterall, it must have a bathroom somewhere right?

This question must necessarily be related to the question what he ate? If a Ferengi can sustain himself on Holofood, and if Holofood procures Holopoop?

I wouldn't think the food would be holofood, the holodecks and holosuites would surely have replicators incorporated into them so that the food and drinks created would be real.

Could be. Then he'd have to eat it all, or there would also be an issue of waste extraction in the holosuites. Would the holosuites as well as reaplicating real matter have the ability to turn real matter into photons? (or whatever holostuff is made up from)

They probably have a real replicator somewhere in the holodeck which serves as the "kitchen" for Vic's nightclub.

The problem with a holodeck potty is the real waste matter is simply covered up by the holodeck program. It is still there, you just can't see it - although after a while you would definitely smell it.

My theory is, in a holodeck toilet, a transporter system simply locks onto the offensive matter while still in one's innards and beams it into space. It would seem to be a good cure for constipation as well.