as most of the people say, it depends on the type of pups you have. The risk of being too close to the strings or too low, it will be lost of presence and clarity (a way of saying). Or too bright and unwanted noises. Everything depends on the pups you have and what kind of sound do you want to have. For example, take the powerful "Number 1"
Number 1 has large strings (a "D" neck with jumbo frets), and 100% stock pups. SRV loved (as René Martínez said) to really dig into the fingerboard. That was a priority for him. Therefore, if you see an image of "number 1" pups, you'll see they aren´t too high. Just a little from pickguard. If the pups were too close to the strings with the kind of strings that srv used, it would had been dirty (opaque or unclear). Well i guess...

sorry for my english...i hope you understand what i want to say.

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"music make peolpe smart..."

You said it all!

I'm not to bothered about my pick-up height, but I've recently been tampering with the height of them on my custom shop '69 strat. I like the pick-ups in it but there have a really 'thumping' sound, and at the same time, clear too. At the moment I'v settled with the bridge pick-up being high and the neck pick-up being lowish.