I assume this is for flotation bags, since you say you’ve seen this method used a lot, and that’s the normal purpose of having lacing across the top of your boat.
As to the diameter of the cordage to recommend, many people just use standard parachute cord. Its diameter is about 1/8th of an inch (so roughly the same as the 3 mm recommended by Pete). You can get it lots of places, though quality varies tremendously. The worst quality parachute cord I ever bought was from REI, but it could be that they buy it from whatever source is most convenient at the time and in that case my experience may not be definitive. The best I’ve ever bought was from Cooke Custom Sewing, but surely there are lots of other quality sources.
If you are making a containment system for flotation bags, the easiest method to setup is what Pete describes, or some modification thereof. Lacing and unlacing your float-bag cage through holes drilled in the hull is a rather time-consuming process (probably less so if you make the holes bigger than I did), but of course that doesn’t matter much if you typically run with the bags installed. If you like to be able to switch back and forth between bags or no bags at a moment’s notice, you could use pad eyes, or still keep it simple and rely on holes drilled through your hull. What a lot of people do is install the parachute cord, not as a continuous back-and-forth weave, but as a series of individual loops passing through the hull (best done by drilling pairs of holes through the hull instead of a series of equally-spaced holes). Then a separate cord is woven back and forth between those permanent, small loops. To accomplish that same thing, when I switched from standard lacing to quick-install lacing, I simply used my existing hole spacing to install a single cord on each side, woven back and forth along the hull, so that cord could be slackened off a bit to create a series of loops, or fully tightened to be flush with the hull and out of the way when the float bags and back-and-forth lacing were removed.
If you are talking about tie-down loops as a way of securing packs or other gear, a small number of loops or D-rings secured to the floor of the boat would work far better than a lattice across the top.