The increased use of fertilizer tends to lead to the forced increase of pesticide use IIRC (Source is in my library at home atm, sorry). It also leads to a decrease in nutrient value from the food as well due to the increased pesticide use.

From a pure efficiency note, pesticide and fertilizer use is the best solution in the short term. But I'm curious what the long term repercussions will be for both human and environmental health.

In the long term, we're all dead :)

But I agree with your point. Sadly, long term is too long to have enough information to make decisions ex ante.

And on your pesticide and nutrient value claims, I'd love to see data on that, sounds pretty dubious to be honest.