I would love to see a way to represent a 3D galaxy, in map and location of the stars.
Well, at a scale usable by my eyes.
You can use a 3D map that looks like this (
http://www.atlasoftheuniverse.com/12lys.html) that can project the 3D positions of the stars onto 2D. This will work with positions of stars but doesn't really help much in visualising borders or regions of space. For a subsector-sized region of space it would work OK without too much clutter.
In practice, it won't really scale up to a large region of space without getting unwieldy. For a sector-sized region of space (about 100 LY across) you would have 64 maps. However, the relatively short ranges of Traveller starships are designed to facilitate sandbox gaming in a small region of just a couple of subsectors. With a jump 2 ship you could easily set a whole campaign in a map with maybe 8 (2x2x2) subsectors the size of the example shown in the link. With the density in the map that would be about 250 systems. You could have (say) 1/3 of them inhabited and have enough worlds for a reasonably substantial sandbox campaign in a region about 50 light years across. You could also build subsectors off the edge of that region as needed.
Past that, you get into using a computer to do the mapping, and build an application that allows you to zoom, move around and look at regions from different angles. You might also need to be able to filter stars out of the view to reduce clutter on large regions.
I'd say modern mobile tech such as an iPad would be convenient enough to use an app of this sort at the table, but it would be a significant effort do develop it. I'm not sure such an app exists as such, and it would require development skills and a non-trivial effort to write. Whether this would be worth your time for your campaign is debatable, and making an app polished enough to publish and support commercially would be a major undertaking.
Unless you really want to go down this route I suggest you stick with a 2D map. I made a decision like this once, although I was doing the game about 25 years ago before mobile technology such as iPads were available.
Given the schematic nature of Traveller subsector maps, they really have to be treated as an abstraction for gaming convenience (after all, GDW was originally a wargaming company). While we have enabling technology now that wasn't available in the 1970s, I don't think the schematic nature of the maps detracts from the game at all.