Of course, if a simulation happens to have some output, e.g. pixels on a screen, infrared radiation from a processor, etc. that doesn't effect the simulation itself.

While it's true that a simulation will be part of the real universe, it's not particularly useful to think at that level; in the same way that it's not useful to handle POSTs to a login form by considering the voltage difference across logic gates. It's much more useful to use the "laws of HTTP", "laws of TCP", etc. to reason about "requests", "processes", "sockets", etc. Such entities do exist, but they exist in a "virtual" world; that world is not separate from the physical world, but it can be completely described without reference to the physical world. Physics and reality are merely implementation details, and don't offer any particular insights into the system's behaviour.

In fact, a computer (e.g. one running a simulation) is an incredibly contrived situation; about as pathological as you can get, since (digital) computers are specifically engineered to abstract away the laws of physics, are robust against perturbations, and their overall behaviour is irreducibly complex (as Wolfram would call it). The only results we can derive about the signals in the computer are trivial, i.e. they would apply regardless of what the system's doing; e.g. the signals aren't creating/destroying energy, they're not propagating information faster than light, etc.

As a concrete example, the statistical mechanics underpinning classical thermodynamics requires that we assume ergodicity (all states are reachable from all other states, with some non-zero probability). We can't make such an assumption for a computer, since it would violates Rice's theorem (i.e. if the "halt state" is always reachable, we've solved the halting problem), and hence we can't apply many of those techniques. We could argue that there will be eventually be errors, like cosmic ray interactions, and we can use their (exponentially small) probabilities to gain ergodicity, but that gives us predictions despite the simulation, not about the simulation.

The only sensible level to understand a simulation is at the level of software; e.g. as instructions, procedures, datastructures, modules, classes, combinators, whatever. If those software components interact such that an "Inhabitant" object's "tastes" attribute references an "Apple" object, then it's completely appropriate to say that 'the simulation's inhabitant tastes an apple'; we can compare/contrast how/if an inhabitant is related to a human, and how its taste attribute is related to humans' sense of taste. In this simplistic example, the simulation would be incredibly crude in comparison to humans and their taste, in which sense we could say the simulation is "low resolution". However, we cannot deny the existence of such simulated individuals, or claim that they cannot taste simulated apples, in the same way we cannot deny the existence of login forms and POST requests. They exist in virtual worlds governed by laws encoded in software and hardware. That those virtual worlds just-so-happen to be implemented by a chunk of the physical world (called "a computer") is undeniable, but it's also almost completely irrelevant if we want to describe, study, predict, etc. such worlds at a meaningful level of abstraction.