Clip, what strobes are you talking about? If you're going to be putting them on your car make very sure you know about any related legal implications in your area.
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How can a thief tell the difference? There are a number of ways. 1st, half of the keyless systems out there don't flash the parking lights when you lock or unlock the door. 2nd, most of the less expensive keyless systems don't use rotating frequencies or auth. codes and as such the signals are easily recorded. 3rd, they know the difference between an old stock security system and an aftermarket alarm, its limitations and how to disable it. Just assume they know.
As mentioned before, if a thief thinks the car has an alarm system, they may pass it up for one that's going to be a quicker job. You'll never know, but just be glad of that.
Personally, I don't count on my alarm to prevent someone from smashing a window, grabbing what they can carry and running off with it. I count on it to page me the minute the alarm is triggered or disarmed so I can get to it before they manage to figure out how to bypass all the kill relays and get the car running or start chaining it up to a tow truck.
For those of you who think it's all just paranoia... I live near a high school, been here over 5 years. My neighbors and I have all noticed that the alarmed cars around here are very rarely broken into where unalarmed cars are broken into almost once a year. My former vehicle was broken into EVERY winter. My wife's was broken into on all but the last. Both of our cars has an alarm now. Less than two miles from my home is a nice, quiet neighborhood. Very few problems, almost no break-ins ever reported... and a small chop shop that was just shut down at the end of last year. Most people were stunned, couldn't believe it... well, you may not be expecting it, but don't act like you're not or you may be the next mark.
Another important tip: Don't give anyone all the details of your alarm system. Don't even tell them what model if asked. EVERY alarm has its weaknesses and once they have the model and know that you've got one additional kill switch they're in business. Don't assume the person you're talking to about it isn't going to do something with the info. The "chop shop" I mentioned above consisted of two "upstanding" families living in two houses right next to eachother. Think you know your neighbors? Don't count on it.