I don't think the fitness of the defence is the main reason for why we look so leaky.
The problem is our centre-halves keep getting isolated because our full-backs push too high up the pitch. They have no-one covering them when they maraud forward.
It's a distinct lack of communication.
If you analyse most of the attacks/goals that we've conceded, they have mostly stemmed from the wide areas because either Guendouzi/Xhaka are too far forward or don't have the discipline to get back and cover for Monreal/Bellerin.
However, another reason is because the likes of Mkhitaryan drift in-field, leaving space open on that side of the pitch and then don't bother to track back when the opposition have the ball.
Despite his 2 assists, Bellerin looked uncomfortable defensively the entire game on Saturday. Part of that was because of his own bad positioning, but part of it was also because he had no-one helping him when West Ham overloaded on the flanks.
We suffered the same problems against Manchester City and Chelsea's winner also came from Hazard having loads of space to run into without being challenged.
Until the players communicate better and have a better understanding of who needs to be positioned where if the fullbacks get forward, we will continue to face the same problems. Emery also needs to tell the wingers to help out more defensively.
Because right now, any team that have pacy, nimble wingers will be causing us a whole host of problems due to how much space they have.
So I would argue it's a tactical issue rather than a fitness one.