The malfunctions/sabotage settings are enabled everytime you start SH3 via SH3Cmdr, so if you go on a 'Shakedown' cruise you can test for malfunctions/sabotage.
Leave port and find deep water. Test crash dive, flak guns (loading times), Engine faults etc...if you find something which is not to your liking you can return to port and reload via SH3Cmdr to get a whole new set of randomised faults or none at all.
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