I'm struggling with this issue right now too. We too are a produce company (also SQF) and some of our loads are also multiple stop but not as many as you have! Module 10 does not specifically require seals, although I have had auditors ask me what our seal policy is. To this point, I've said that we do it if it's a customer requirement. But I am in the middle of developing a policy that we requiring ALL incoming and outgoing loads to be sealed. Still not sure if I'm actually going to roll it out as I know I'm going to get major flack from my shipping, receiving, and procurement departments; precisely for the reason you state above.
Also, we've recently had some loads stopped by either DOTs or Police, who have broken seals and searched loads (with dogs!!); looking for drugs I guess. How do you manage that risk?? This just gets harder and harder. I think I soon need get a job where I just make one thing for 8 hours a day and then go home.
So, yeah, kind of in the same boat as you.