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It depends on the game and emulator. Some emulators have emulation inaccuracy that would cause you to be able to achieve things said emulator that would not be possible were you playing on official hardware. As one example, some emulators do not handle the random number generator the exact way it would be handled on official hardware, meaning it's possible to encounter a Pokémon generated during an RNG state that isn't possible to achieve otherwise. Some GBA/NDS emulators I remember had issues dealing with VBLANK and were generating Pokémon in Gen 3/4 games with stats that couldn't not legitimately be encountered except when playing on an inaccurate emulator. (PKHeX is even able to catch these "impossible" Pokémon during legality checks, flagging them for PID mismatch, as their stats don't match any possible RNG state the game can produce.) As another example, BDSP uses the Switch's internal clock (the RTC) to determine whether when time-based events should occur, and whether to incur a penalty for trying to alter the clock. On our Discord server, we determined that current Switch emulators do not properly emulate the RTC and was not properly assigning the date/time values within BDSP's save structure. TLDR Yes, you're likely to have minor inaccuracies, you just have to hope they don't occur anywhere that would set off red flags, so to speak.

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Thanks! Just hatched my first shiny yesterday! ^^