I would much rather ditch a rocket / missile launcher than my combat/tactical/assault shotgun. It may be possible to live without it, but I would rather not. Fair enough that the double is usleless without shell box, but for others, 5 or 6 shots is enough to deal with pain elementals.
Two other points:
The original poster asked about early / midgame / late game weapons:
MAc - Shotgun > combat shotgun > plasma
MCe - Shotgun> chaingun and combat shotgun > plasma (early EE makes a huge difference)
MEn - shotgun > combat shotgun > plasma
Note that I may switch to the chaingun at any point depending on the map. The chaingun is generally better on the maze of rooms maps, where you are more likely to have several enemies approaching you at medium ranges from different directions. But I would say my bread and butter means of dealing with difficult enemies is shotguns of one sort or another and corner shooting until I get plasma. Chainguns remain in use throughout the game (until nuke plasma rifle) for dealing with formers and the like.
With respect to ammo, obviously for MAc its a no brainer. For the other two rapid fire builds I would say 2 stacks of shells, 1 stack of rockets, and a TOTAL of five stacks of 10mm / plasma. However, in the early game if you plan on clearing the court and the wall carry as many rockets as you can, rockets are the best means of dealing with tough enemies at long range before you have enough traits to be dangerous with rapid fire weapons. As the game goes on you can replace 10mm with plasma, and once you get the nuclear plasma rifle you can ditch plasma completely. All of the rapid fire builds should be able to clear spider's lair pretty easily.
Also - the new assault rifle sucks. It doesn't even remotely compare to the old one - it uses more ammo, fires slower, and is less accurate. The old assault rifle allowed rapid fire builds to be as efficient as a pistol user when it comes to ammo consumption. The new assault rifle just slightly increases your damage per bullet and slightly increases accuracy, at a cost of less damage. It is not worth it in the least. The assault rifle wasn't a complete no-brainer - the old tactical boots / armor could be worth it. The new assault rifle is really the hyperblaster - it is even more of a no-brainer than the assault rifle because you can use it all the way from when you build it in the armory to level 24, whereas the assault rifle was more of a mid game weapon whose main advantage was ammo efficiency.
Any and all rapid fire builds benefit from the hyperblaster. There are better weapons if you get exotic weapons or mods, but the hyperblaster is worth basically 3.5 tech mods, 2 power mods, and 2 agility mods. Plus it benefits twice as much from triggerhappy compared to a vanilla plasma.