When you have questions like this, the answer is almost always money.

For this particular question, it is money - the cost of the LEDs (which is of course minimal, but multiplied by millions of phones), but also manufacturing (need to have a hole in the case to let the LED shine though which can let water ingress into phone). To make those holes water tight would add more cost so instead they decided to use the screen itself as the notification method. I think Motorola's implementation of this was the best - they had their always on display to show notifications and a single tap would let you see what the message was even if the phone was locked.