Is there a rule of thumb regarding the sizes of portholes? What about the width of catwalks and height of the guardrails? Average width of walkways between the superstructure and railing (IOW the side of the ship)?

Most Naval ships these days don't have portholes.

My apologies, I meant non-warship vessels.

Portholes vary significantly...the only standard that I think you'll find is external water-tight doors (WTDs). Not sure of the dimensions, though.