Ali,
I have seen the spotter planes! the thought of "the fish are simply being depleted" is Heartbreaking! I hope this is wrong!
To be my best knowledge i think the reason of tuna gone missing is not only over fishing but also the change in sea temperature the global warming effect. Tuna migrates annually to spawn in warmer waters of Arabian/indian Ocean and spawn in Tanzanian waters (ref book: The Tuna), fishermen have been tracking them since early 19th century and if we look at their heaps of records.
One of the most neglected matter is the cattle dung dumping in our ocean. We have 400,000+ cattle in the patch of 3X3 KM of dairy Colony near Landhi making it the world's largest dairy colony. Now as well as producing milk these animals also responsible of making over 8000 metric tons of dung every day, this is enough to cover the area of 119 squire kilo meter which is good to cover whole Karachi in .5 inch of dung with in 29 days, this is my made area fact by using the numbers provided by nzaid.govt.nz as they conducted this survey

and yes this can also generate over 40 mega watt of electricity every day… watta misery.
Now this creates loads of Methane in atmosphere and chemical bloom in our ocean, traces are found till Ormara and Khadda. With the help of a friend of mine in desalination business I’ve even conducted few water tests and found that COD/BOD rises to create water almost oxygen less, dragging our ocean towards a dead zone (ecology) see wikipedia. Low oxygen means decreased size of reproductive organs, low egg counts and lack of spawning and ultimately no fish = dead zone.
This become worst in monsoon when rain flush out huge amount of dung which normally move very slowly because it’s high in viscosity
Don’t forget the same waste produce by 18 million peoples living in Karachi and the huge industrial area dumping everything in sea, it makes me feel crying some times watching all this helplessly.
For information a huge dead zone is already marked by intl. marine biologists exactly in front of Indus delta. It can be seen in goggle earth after activating the marine layer.
The traces of dung flowing in mangroves can be seen from satellite near rehri goth, see google earth.
Another reason could be the bait fish utilization in Poultry Feed, here are the shocking numbers:
Pakistan fishmeal production was about 65,000 to 70,000 tons, compared with 30,000 tons in 1985.
252 hatcheries, 141 feed mills and 13,154 poultry farms with the capacity to produce 98 million chickens. [Ref: Pakistan Economist]
This is over 500 thousand tons poultry meat!!!
AND THEY NEED BAIT!
These figures speak of the potential!!!
This is all harvested from the wild, obviously they don't catch commercial fish for fishmeal but the bait and since bigger fish feeds upon the bait fish therefore we are witnessing the depleting Tuna, Wahoo, mackerel etc. etc.
UNSUSTAINABLE!
From the link:
Pakistan Game Fish Association | Fishing Report