The Ninja/Samurai/Pirate Ship Build is collaboration of many ship builds into one. It combines slow ranker, hacker, raider, SSB, and well rounded ship builds. Here are the things you need to have this ship build.

1. In the endgame, the only things installed on your ship are % mods, ability mods cloaking and scans.

Reasons:
A. You may have all these things if and only if you are efficient with your ship crew.
B. That is because having all scan and cloaking mods uses up a lot of deck space.
C. Every other module that I have not mentioned are worthless and place holders for worthless increasing upkeep and inconvenience overtime.
D. Some things eventually outlive their usefulness and become rusted in time.
E. Because there is absolutely nothing to increase the strength of researched modules overtime, they are meaningless, dead weight in the endgame in the galaxy filled with artifact production.
F. In the endgame, every single mod I listed will no longer need to be switched around in order to go on a planetary scan run or badge run with less upkeep.
G. The total upkeep of all modules that I have listed have lesser upkeep and is more efficient in the long run.
H. Besides, there still is not enough efficient modules I have listed to fill up all the deck space needed in the damage cap in the endgame that does not lose its shelf life overtime.
I. It is alright to do missions if and only if you can maintain your ship strength and prepare to increase your artifact production before ranking.

2. Have good artifact production.

Reasons:
A. It is best if your crew is not lagging behind and always at it's prime from good artifact production.
B. Every single crew such as tactical officers, helmsmen, engineers and scientists for easy raids.
C. Slow ranking is highly recommended when hiding as a ninja ship build with all these scans and cloaking mods on.
D. We will never be sure entirely of what new mods with scans and cloaking will come out, so be prepared for deck space increases.
E. With good artifact production, you could also make sure that your durtanium brackets are your main sources of increasing hull.

3. Your final goal in research is to finish off logistics for it's base upgrading and mainly its universal terminal.

Reasons:
A. Base artifact production is also important as well because eventually at some point in time when you get more artifact production without it.
B. The universal terminal is key to having all of the special abilities at the grasp of your hands to use in any situation.

This sounds quite a lot like the goal I set for my ship ( Subject: Peticks ship log, rank 610 and counting
) , although I plan on having enough room for all scan, or all cloak, or all % and ability mods at any one time. So float around with all the % and ability buffs for normal day to day but when going on a scan run switch up the setup. Saves at least a thousand decks I would think. Though, when your ranks high enough eventualy your ssb cap will be such that you can go full scan, cloak and %/ability mods. Essentialy though I wouldn't say that if you aim to have all scan cloak and bonus mods installed that slow ranking would realy be that big a part of it