Actually the same exact thing happened to me, I had all upgrades except the elite fire barrel storage. I was missing it because you get it from the kenway fleet thing, which I never did at all so at that point, and I tried fighting the the impluto and it killed me so did the twins but I came close on them. Said forget it when and did some other stuff include the kenway fleet and got the one missing upgrade. Went on to beat all 4 first try with minimal trouble. Only the one with armor took 2 tries, I watched a video on ramming it, did what that guy did and won with ease compared to how I was destroyed not long before. Didn't think anything of it but it could be you maybe get a little all around bonus when you have everything like you said. Or it could just be coincidence.