Not necessarily. For example, if there is custom hardware used for communications with other systems, such as radar for example, there might be specific timing and latency requirements that could be difficult to meet under emulation.
The most recent Dolphin Emulator post referenced a bug they had where memory cards were written to too quickly under the emulator (and even on actual hardware if you had memory cards that were sufficiently fast) which caused some games problems because they did not expect save files to be written so quickly. Imagine things like that, but where the worst case isn't having Wind Waker hang while saving, but planes crashing.
The most recent Dolphin Emulator post referenced a bug they had where memory cards were written to too quickly under the emulator (and even on actual hardware if you had memory cards that were sufficiently fast) which caused some games problems because they did not expect save files to be written so quickly. Imagine things like that, but where the worst case isn't having Wind Waker hang while saving, but planes crashing.