All right, I said in the review section that I would explain my thoughts in detail, so here they are. I hope the wall of text doesn't crush anyone. :P
In your example about Damage Up and Defense Up, the numbers you chose don't quite illustrate your point accurately. The game actually does measure damage numbers beyond whole numbers (and possibly even beyond tenths--more on that later), so 99.64 would not simply round up to 100. This is a very minor error, but I felt obligated to point it out.
I personally would not simply dismiss Defense Up as a "rare ability" for the simple reason that some players focus on fashion rather than abilities when choosing gear. These players are unlikely to have a large amount of Defense Up, but it's not uncommon to see, for example, 1 main and 1 sub of it. It's something that I feel is worth keeping in mind.
With regard to Burst Bombs, I think it would be helpful for you to include the numbers on the different hitboxes they have. With no Damage Up or Defense Up in play, they can deal 60 damage (direct hit), 35 damage (near miss), or 20 damage (graze), and nothing in between. (In theory, this means that the base damage is enough to splat with 3 indirect hits, though that's unlikely.) This is important because it creates distinct thresholds of what you can do with Burst Bombs, especially when you use them in combination with your weapon's main attack. (Again, I'll explain more about this later.)
Regarding Chargers, I believe I've seen it mentioned somewhere on these boards that even with 3 main Damage Up abilities, the Squiffer's minimum charge to splat is only lessened by 1 frame. Take that with a grain of salt, but if it's correct, it would mean it's probably not worth using Damage Up with the Squiffer.
You're right that most Shooters don't really benefit from Damage Up, but there are a couple exceptions that I believe are worth pointing out. The .52 Gal and the Splash-O-Matic, unlike other shooters, can have their hits to splat affected by just a single Defense Up main ability, and, as I said before, it's actually not uncommon to encounter that amount of Defense Up. As such, I believe that preemptive Damage Up is actually useful for those two weapons (especially the .52 Gal, since the 2-shot splat is its main selling point). The Splattershot may also be worth noting, since it can be affected by 2 main abilities or 1 main and 3 sub abilities of Defense Up. It is possible to incorporate this amount of Defense Up into an Ink Resistance + Cold Blooded/Ninja Squid set without an unreasonable amount of re-rolling, and since the Tentatek Splattershot is so popular, I could see a few serious players deliberately crafting such sets to counter it. (I actually have one myself, though it's not quite perfect yet.)
Now, I mentioned earlier that there was something I thought you could add that would be helpful. Unlike other abilities, with Damage Up, the exact amount of the ability you have can actually be quite important due to its effects on your hits to splat. As such, I think it would be very helpful if you included some thresholds of what sort of things you are capable of with varying amounts of Damage Up; this would help people to figure out exactly how much Damage Up is right for them.
I've spent some time at the testing range figuring out some thresholds I've found useful for my own sets. (Remember that 1 main ability is slightly stronger than 3 sub abilities.)
.52 Gal:
1 sub Damage Up = Maintain 2-shot splat vs. 1 main Defense Up
4 sub Damage Up = Maintain 2-shot splat vs. 2 main Defense Up
1 main + 3 sub Damage Up = Maintain 2-shot splat vs. 3 main Defense Up
Splash-O-Matic:
1 sub Damage Up = Maintain 4-shot splat vs. 1 main Defense Up
4 sub Damage Up = Maintain 4-shot splat vs. 2 main Defense Up
1 main + 3 sub Damage Up = Maintain 4-shot splat vs. 3 main Defense Up
Splattershot (shots only):
2 sub Damage Up = Maintain 3-shot splat vs. 2 main Defense Up
1 Main Damage Up = Maintain 3-shot splat vs. 3 main Defense Up (Note: Although the testing range dummy shows only 33.3 damage for a single shot, 3 shots will somehow add up to 100.0 and splat it--hence why I said the game seems to measure damage beyond even tenths.)
Splattershot (shots + Burst Bomb, assuming no Defense Up):
2 sub Damage Up = Splat with direct Burst Bomb hit + 1 shot
1 Main Damage Up = Splat with minimum Burst Bomb Graze + 2 shots
Slosher (slosh + Burst Bomb, assuming no Defense Up):
1 Main + 1 sub Damage Up = Splat with minimum Burst Bomb Graze + 1 slosh (Splat with Burst Bomb near miss + 1 slosh is possible without Damage Up.)
Again, sorry about the wall of text; I just genuinely want to help, and I believe that this guide has potential, provided that you have the will to refine it. I hope what I've written here will be helpful in some way.