No offense meant, gentlemen, but I'd say you're not entirely correct here, while I'll admit I'm basing my experience on a 97 and a 99 Boxster.
Yes, if the car immediately beeps at you upon the button press, that means something is unsecure (as mentioned, doors not closed completely, a trunk open, or the center console lid not closed).
However, to my knowledge the horn beep of the alarm is a programmable function from the dealer. The short horn beep a few seconds after the car is locked via the remote can be turned off, which is likely what the previous owner had done here. I'm not sure that the light flashes can be turned off (two flashes indicating locked, single flash inidicating unlocked, long single flash indicating locked with IR sensors deactivated), but I know that the quick horn beep can be turned off.
If you want to test it, roll your windows down (with the top up), lock the car, and reach in and wave your hand around near the dash to see if the alarm actually goes off and beeps the horn continuosly.
The other possibility is that your alarm horn (separate from your idiot repellent horn in the steering wheel) could have gone bad and needs to be replaced. It's up by the battery on the driver's side under the plastic mesh covering.
Also note, the lights will not flash when you use the key in the door to lock/unlock the car, though the horn will still beep if the car is programmed to do so/horn is working. A few seconds after that, you'll see the LED in the dash flashing to tell you the IR sensors are active, as you also should when you use the remote to lock the car.
I don't know if they changed it from 2000 onward, so if my info is incorrect in that case, then don't let me misinform you.
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-O/D
1997 Arctic Silver Boxster, 5-spd
IMSR + RMS
Robbins glass window top
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