Squat-wise I have done nothing but low-bar from 140 kg x 1 up to 200 kg x 5. My quads look pretty similar to kingfish's. So no, I would not say that low-bar squats will cause you to miss out on quad strength. My first real front-squat work-out was 140 kg x 3 with more left in the tank - so low-bar carries over just fine, as will any strength exercise that works hips and legs through a nearly complete ROM.
People always forget how progressing in a given exercise is actually much more important than which variant of the exercise one is performing. And most people will outperform a high-bar progression with a low-bar progression easily, because you can just manage more weight that way, so the ceiling is higher, and you involve more muscle mass. Low-bar squats done correctly are an insanely good exercise for every kind of athlete.
I'll give you that specificity is pretty overrated and that even if one "looks" more like jumping that's a silly reason to do it with large loads.
Your front squat ratio (assuming ~140kgx 5 since had more in the tank) is 0.7. Much better than most powerlifters, but I would still expect high bar squatters to have a higher ratio. Myself I maxed at 315 lbs in the front squat when my back squat max was only 370 lbs. Still, a couple people don't make an argument.
The main advantage to high bar squats is that they do translate better to olympic lifts. You just can't catch a clean or snatch without knee flexion. You just get lower with the high bar squat and if you want to do full olympic lifts then I really can't see why you would avoid high bar squats.
Besides, the olympic lifts your argument seems pretty solid. I don't have any REAL reason to dislike low-bar squats......But... I just feel like I have seen many more people have a really impressive low-bar squat while at the same time having poor deadlifts, vertical jumps, speed, etc. I have no data whatsoever to back this up, it could just be a function of the fact that the low bar squat allows everyone to handle more weight, or maybe because powerlifters do it and they have a propensity to be uncoordinated fat slobs.... But in my experience is less likely someone has a good high bar squat and is terrible at everything else. Really, I try and get everyone to at least BE ABLE to do both. ie. If you can't squat a couple plates high bar and low bar somethings wrong. Once you can do that, then I guess it doesn't really matter which you favor.
I'm also very suspicious of the term low bar squat. I've never seen you squat but since I know your an athlete concerned about your vertical I'm sure your low bar squat has a somewhat narrow stance, has some knee flexion, and probably has decent depth. It might be that this kind of low bar squat has a lot of benefits, but powerlifting has created somewhat of a perversion of the low bar squat.
For example heres a low bar squat that I bet would translate pretty well to athleticism:
http://www.youtube.com/watch?v=fivhv5znPg0This one not so much:
http://www.youtube.com/watch?v=UikcjCBN34Q