I'm assuming that best practice is to build in security features as you go along to preserve the integrity of FM, DM, AI behavior, access to rare or advanced equipment, terrain and weather generation, and so forth, but I'm utterly clueless in this area. The SAS mod team are the folks to talk to.
For a "sandbox" type sim like you're designing there is an inherent tension between player freedom to modify the game environment as they wish vs. screwing over other players. Obviously, cheating is no big deal for offline solo play (other than people posting and complaining about videos of grotesquely modded aircraft on Youtube), but it's an absolute deal breaker for online and/or multiplayer play.
I think the best ways to deal with stuff like that is transparency (i.e., make it hard to hide evidence of cheating) and having a "referee" who can lock down certain aspects of the sim during multiplayer play.
Depending on how sophisticated you get with FM and DM, you might also be able to have unchangeable elements of the game which are based on a given airframe's physical model so that cheating becomes impossible. For example, any attempt to soup up the FM of a Sopwith Camel to give it the flight characteristics of an F-16, or vice-versa, is inherently doomed to fail because the airframe of a Sopwith Camel or F-16 will still "fly like it looks" rather than "how it's programmed." Even with the Sopwith's engine output and mass fudged to mimic that of an F-16, you might still have problems with landing gear collapse, extremely long takeoff run, huge turning circle, lack of fuel tankage due to smaller volume, and so forth.
It might also be possible to build hard, realistic limits on historical aircraft performance into the game, with limitations to things like construction methods, drag, fuel consumption rates, compression ratios, or power/mass ratio for engines set by year. That way, if you really want to fly something that looks like an F-16 in a 1918 scenario you can do so, but its still going to behave like an aircraft built in 1918 - that is, not very well at all.
Conversely, if you want to fly something that looks like a Sopwith Camel in a 2018 scenario, but which is made with state of the art technology, you'd get something much better than a 1918 aircraft but that's still no match for an airframe designed to take full advantage of modern tech. (That said, being able to model duels between modern kit-built imitations of historic aircraft might be fun, especially if you've always thought that the Oshkosh Fly-In would be more interesting if live ammo were involved.
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