So I've been struggling with defenses the entire game, the researchable modules just seem to take up so much space for so little defense. It hasn't really been all that important up to this point but now that I'm getting up near the mid-100s in rank things seem to have changed. What is the best way to add defense to the ship without taking up a ton of space? I rarely get android helmsmen from arti pulls but I'm thinking about going ahead and using rank points and prisoners for defense, would this be foolish?

Yeah. Don't do that.
Atk or energy only.
If you want to raise def raise your arti.

Btw what counts as msb for someone that low?

Currently I'm sitting around 500 decks, and I have no plans to add any for some time. I think that's why the defense modules seem so space consuming...

As a partaker of the MSB class, personally, just add all 8 defences, it makes things a lot easier, without def you might as well try to drop to SSB

With his current setup that's alot of decks.
Id bet npc mods would be the way to go.

ATM I have 2 Dark Ring Thrusters, 3 BM50 Convoy Shuttles, and the auto evasion node equipped... Are there any mission defense items that would be worthwhile to go for -- and which NPCs drop defensive modules?

It really depends on how hardcore you are going to be as an MSB, sure everyone wants to be Golg, but very few can manage his style without ending up with a poor ship. I'm probably nearing the high end on decks for an MSB, however I've been noticing a huge SS boost on most of the others trying to do the same

List of NPC dropped arts You can find the defenses ones on your own.

As for whether or not to add defense or not. In a word at your size/rank no. The point of a MSB/SSB is that they take more energy to kil you because of your size and hull. Someone with 2k decks uses their defense to increase the amount of energy the other person has to use to kill them by making them debuff or hit at much lower % of the damage cap. You on the other hand use the fact that the cap is there, so you gain more hull/shields to make them expend more energy. defense will come on its own later, what you need is more hull so that the min # of shots to kill you is higher that way they are forced to spend so much energy they can't kill you. (this is for people your rank).

Personally energy means nothing to me, I kill golgotha on special occasions for the fun of it. Also exotica, but usually bt.

Sooo, adding tons of Hull would be a good idea.

rank 100 with 500 deck huh? I'd go about ~2 rank point into deck per rank until maybe 1200-1600 deck, then use shipbot only.
before rank 400/deck 1500, chances are you are not gonna use much researched def mod as they are not very space efficient AND your deck will probably(at least in part) come from rank points, making it very "expensive". instead you should look for NPC/mission/battle market stuff. After that thou, you can probably do a % calculation in term of increase in def vs increase in deck(both % ratio). Personally, I add deck to have the module if the % increase in defense is at least twice that of deck. While therotically helmsman will make it so the ratio become smaller and smaller, two times is safe enough(by the time you get enough helmsman, you will probably get better modules to replace the def ones from missions or NPC)

I'm already at the point of only adding decks with ship-bots... For some reason I get those in abundance LOL. I think that next I'll go for the biomimetic sealers as those will add both hull and defense. I haven't bothered with them yet because I'll have to change profession for the install but I guess that could work out in my favor and I'll finish off getting these last 2 dominion-mk III's.

I'll help you out with your actual question being that im in your rank range. Currently sitting at 480 decks. The mods you want to install as soon as possible are

Dark ring thrusters x 4
Auto-evasion node
Velox Thruster x 3
Trinity Core Drives (if you can afford the GP) x 2

Only install the BM50s if you have 20 space you aren't using. Eventually you'll upgrade the dark ring thrusters to dark phase engines but that's not for a good 160 ranks or so.