So here's an interesting place to set a sci-fi campaign. Boötes II is a galaxy located pretty close to the Milky Way at only 137,000 lightyears away or so. It takes the form of a roughly spherical cluster of stars only 72 to 102 parsecs in diameter. That's its half-light diameter, at least. You could lay out some more stars past that sphere, but either way the point remains that Boo II is friggin tiny. A circular slice of this place that cuts through the centerpoint could fit on only 2 or 3 Traveller sector maps! For simplicity's sake, I'll set the effective radius of Boo II at about 32 parsecs or two sector maps placed side by side.
Mapping a third dimension for this galaxy would be relatively easy. Just imagine a stack of 40 pairs of sector maps. The middle two are full-sized sectors. Label those Z-1 and Z+1. Above and below them you mark through the three outside edges of the map before you stock it. Those are the maps for Z+2 and Z-2. For Z-3 and Z+3 you remove another two rows and single column from the outside edge of the hexmap. Repeat until maps Z+20 and Z-20 are only two hexes wide and 13 hexes long per sector map. Those are effectively the north and south poles of our galaxy.
You could stock Boötes II using the standard Trav method of a 50% of all hexes contain a star with some sort of randomly generated world. Running numbers of yields a galaxy of not quite 11,000 hexes with over 5,000 stars. You could play with the stellar density a bit. A low density galaxy where 1 in 6 hexes are occupied would get that number down to less than 2,000 worlds to dice up.
But there's another interesting option: keep the stars and ditch the planets. The real Boo II is a low metal galaxy with only one eightieth the metallicity of our Milky Way. The usual astronomical definition of 'metal' is 'anything heavier than hydrogen'. So only one in eighty of those stars will have a solid world or asteroid belt around it. The rest will be bare or orbited by things like brown dwarfs, the latter being a tremendously useful fuel source under these conditions. So keep the 5,000 stars on your 80 sector maps. Only 60-odd of them have planets actually worth talking about. Put that in your Drake equation and smoke it: only 5 dozen worlds you can actually set foot on in the entire freakin' galaxy.
Under these circumstances a decent trade route between worlds will probably involve a circuitous 3-d zig-zag of a route through systems with brown dwarfs and/or hideously expensive refueling stations. Most jumpships will be built with the capability of storing sufficient fuel to make 2 jumps, as so many routes between worlds could involve a stopover at a naked star somewhere en route. Maybe some ships run with 'hot' fuel scoops and can actually skim stars for fuel. Watch out for flares, dude!