I think you have enough ideas there Patkhoo to start a few threads of your own.
Heh, why worry about LRM spam when there are these idiot thread hijackers on the forums?
My apologies.. 
But back to topic, my suggestion is instead of looking at queuing "stacks", the code could be implemented to go lower down into queueing and matching ships to targets from one "stack/group/fleet" to another. In this way, the programmers don't have to change too much of existing code mechanisms for queuing/targeting but yet still make it more reasonable to handle many stacks..
I can appreciate the point about memory usage increasing when suddenly ppl queue 50 ships in just five clicks.I don't know how it is in code currently, so I guess Blair will have to figure it out. But if the current code (when you target a whole stack) "expands" the stack into individual ships then assigns the individual ships as queued targets, then this is what I'd call a "design" issue in code.
EG: Stack of 10 LRMs -> target/queue -> stack of 10 frigates
LRM 1 -> Frig 1, Frig 2, Frig 3, ... Frig 10
LRM 2 -> Frig 1, Frig 2, Frig 3, ... Frig 10
LRM 3 -> Frig 1, Frig 2, Frig 3, ... Frig 10
...
LRM 10 -> Frig 1, Frig 2, Frig 3, ... Frig 10
Clearly, this design will have scalability issues. That's why I suggested that the stacks be broken down ships matched individually instead of focus-fired.
LRM 1 -> Frig 1
LRM 2 -> Frig 2
LRM 3 -> Frig 3
...
LRM 10 -> Frig 10
The code change for this should not be too drastic I think. The devs need to balance the idea with how much change/complexity is needed in code. But if you can spend more dev time on a more complex solution, you can try this:
LRM 1 -> Frig Stack
LRM 2 -> Frig Stack
LRM 3 -> Frig Stack
...
LRM 10 -> Frig Stack
And then in the code where the ship LRM x chooses the target, it looks at the queue and sees "Frig Stack", at that point it goes into "Frig Stack", see what ships are in there (dynamic) and picks a target (nearest/weakest/random)..
I figure in this way, the design is more scalable especially for the "worst case" of multiple stack target/queue multiple stack.
Please accept my apologies if my understanding of the problem is wrong. And also, I note that this does not really help the situation where you use one ship and target many stacks.. Probably there must be a fundamental limit of how deep a queue is for one ship. If that is the question of this thread, then I think the devs should make that choice in their best judgment and users should just accept it. This is because it is related to memory and software stability and I think that is more important than gameplay. No point having excellent game play if the machine crawls or software crashes. (sorry, I'm a programmer, so I tend to defer to other programmers 