Ah yes, those darn ninja assassins everyone on gun boards seem to be dealing all the time.
If you see an intruder, lighting him up with a high lumen flashlight and issuing a verbal command seems to be a fairly good idea. If there is enough light for target ID, there should be enough light to determine if the subject is armed. All this supposes you see him before he sees you. If someone gets the drop on you, the question of whether to issue a warning is moot, nicht wahr?
Of course some here will say it's legally better to just kill an intruder. I've even seen a thread suggesting if you need to shoot someone on the street you should kill all witnesses just in case they're part of a gang who could ID you for reprisals. I really wonder how many of the people suggesting these things have actually killed someone themselves, or even seen a person die violently.