Yep, between the simulation issues and the hindsight, you'll always end up doing better. I would actually say that the #1 factor is purely a human one - a game can never completely simulate the uncertainty and fear, because you can't "really" die and once you know the game well enough, you can usually predict how the game and your enemy will behave in a certain situation, or what you will be able to get away with. The predictability combined with the player's ability to endlessly retry usually means that you can usually "beat" what the game throws at you, something that real submariners only ever got one chance at.
The best way to get around it is setting house rules. Every time I play, I develop both a list of things I'm allowed and not allowed to do, and a set of "random" restrictions that I'll use dice rolls to decide as I play. For example I'll roll dice to determine priority targets and the aggressiveness of my approach when attacking TFs, or whether I will pursue a random map contact or not, or where I will look for contacts after my main mission is over. It keeps the game much more interesting and unpredictable for me, and the net result is usually lower tonnage. I had a Type II career not long ago, for example, where in 10 patrols I only sunk three ships.
I just always treated SH3 as a solitaire experience game, not a competitive game. The more unpredictable a career is, the more fun. I honestly don't get why tonnage should be such a focus, especially in a game where you can never "win" the war anyway, no matter how well you do
