Your spoiler layout pretty well illustrates my frustrations with this mech, ammo in both arms & all 3 torso locations, it's rare that a missile boat is getting hit for critical - at the same time it is potentially possible and that layout makes for a walking bomb.
I think you're making somewhat contradictory or at least conflicting statements from my point of view. You seem to worry a lot about where the ammo is located, while at the same time you feel JJs are unnecessary. I as see it JJs survivability value far exceeds six tons of armor. It just skyrockets, and that's for a very long range mech with indirect fire, very good armor for a full-on LRM boat and with the tools to effectively fight at near maximum range while bulwarked behind a tree which is hidden behind a very big rock, with 30% non-removable evasion and capable of jumping out if something more dangerous than an adult squirrel comes too close.That being said, while I agree that Jump Jets would be nice, I don't see the need for an indirect platform to devote space and or tonnage to jump jets.
Anyway JJs imo are not really needed because survivability is already excellent without them, like @foamyesque points out it's more of a QoL feature. I don't use them in the Highlander LRM boat but I've used them in a King Crab LRM boat, used as a trainer mech pre 1.9 and where maximum survival is a priority, a crucial part of their role, which is to keep newbies alive in a mech with high armor, jumpy, very good cooling, no direct LoS required, 3-4 TTS and acting as light-medium rearguard support.
For me, unless I specifically want to avoid using JJs as a handicap, I see them as very important in almost every heavy, assault and many mediums. For LRM boats though, they don't help for offense, only for defense, which while potentially useful usually is not really needed because they're not in the front line. But for most other setups they do help both in big way, very often at the same time. That can very easily end in more real damage being done over the course of the mission, because you get sooner where you need to, opening windows of opportunity to attack vulnerable foes before they bulwark, get into cover or from the back, there is often less risk involved too because you know you'll have a much easier time getting away when you're at a local number disadvantage, and you can return fire while you back down, sometimes turning the tides on that side of the battle as you do it, and without requiring additional support from other mechs.I love some jets on a mech like the Annihilator where setting up direct LoS and or firing from cover are important, but I don't see it as high priority here - especially with virtually every crit slot filled.