In this case Texas defines "criminal mischief" in three clauses, and separately defines circumstances under which it constitutes a felony. Felony mischief is largely but not exclusively defined by the amount of pecuniary loss.
The first two clauses are destroying property and damaging property in a way that causes pecuniary loss to anyone.
The third clause is making marks on property. This seems like it would always be included under "damaging property in a way that causes pecuniary loss", so I would guess it's there to make it completely explicit that graffiti counts as criminal mischief.
The quoted section of the penal code does not appear to apply any restrictions to the specific variety of criminal mischief that justifies deadly force (other than that it occurs at night).
For something like graffiti where the general sentiment is that deadly force shouldn't be considered justified, I could see an argument that the use of deadly force violates §9.42(3)(A), which requires the person using deadly force to reasonably believe that the land or property in question "cannot be protected or recovered by any other means". If we view both verbs as applying to criminal mischief, you could make the argument that when you catch someone spraying graffiti on a wall on your property, your property can be recovered, though not protected, by e.g. repainting the wall.
The counterargument might be that "recovered" is in there as the appropriate verb for cases of theft, and "protected" is in there for cases of mischief.
I don't think restricting §9.42 to felony mischief would be an improvement to the law; it's difficult to know whether criminal mischief is or isn't a felony until you've tried to recover from it and learned how much that will cost. If you catch someone keying your car, for example, that probably is a felony, but as far as social impact I would rate it similarly to graffiti.