Well, in Onslaught matches the Healing Bubble Method isn't even a good Idea, as it is important to get as much Points as possible for your Team by killing other ships, You are not getting anything by sticking together and doing nothing. About the Idea of healing Bubbles in a Conquest game I hope I don't have to refer here (as there must be the goal to take as much place as possilbe, so to all the Players that read this: Please be the nice and SPREAD OUT when getting in such a Game).
Only in a Team Elimination match the Healing Bubble is indeed very effective. So (If you have the patience) you might be able to minimize the risk of getting to deal with a Healing Bubble by selecting a Game mode where it's tacticaly stupid to stick all together.
But in Team Deathmatches I would say that a healing Bubble is the best tactic you can take. So don't complain about healing bubbles in TDs, try and get you team to make one yourself. Usually you can use the communication shortcuts like "need reinforcements" or "regroup near me" or "need healing here". Or you can write a message to your team by pressing Shift + Enter and Typing something like "Stay close together all".
If the devs may have the fun and plan to overhaul the Communication shortcuts, I would prefer a way to say "Spread out" to get the Bot ships take some place so they are not ruining your Conquest match by sticking all together near the Spawnpoint. This command would be also helpful to make your Friends flee from you when you realize that a Nuke is targetet onto your ship. And in my Opinion there does only need to be one option like "Regroup near me" and "Need reinforcements" as they are saying actually the same Command "lets gather here"
And about Methods to minimize the damage caused by a Nuclear strike: I for myself wouldn't even prefer Laser or Pulse anti Rocket or Anti Nuke Systems, as they are often too slow in thier work (especially with these fast incoming warp rockets). In many cases you might save your ship, but getting the nuke to explosion right next to one of your friends who will surely be absolutely thankful for getting the damage instead of you (Usually this problem occurs when a Tactical or Artillery Cruiser starts his anti-Nuke-Laser in the second battle row.) Its a way better method to raise your shields right the moment when you get the acoustic nuke warning. This Method will drain your energy, but in this way I was able to endure a Nuke strike with an Artillery Cruiserand getting nearby no damage. And you have the Space of your tertiary Module for something more useful.