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I cannot speak from personal experience, but yes, i believe they can. Think of it this way... I have ADD in a hardcore fashion. I'm also a pretty smart guy. However, my brain's lack of ability (due to chemistry issues) to concentrate make it very difficult for me to express ideas sometimes. Should I then believe that, by fixing that imbalance with a drug targetted to ADD, I will still have this problem and will not have clearer thought?
Secondly, our brain's ability to "perceive" is also somewhat social. Look at alcohol. When one is sober, one might find a particular girl gorgeous, but wouldn't talk to her to save his life. While intoxicated, the lack of inhibition, in part to the person's new opinion that he might get lucky, he may very well go up and talk to the girl. While this may not (or may) be a religious or spiritual experience, the point is that brain chemistry does indeed alter how we perceieve things.
Lastly, assume for a moment that the human brain is only roughly 12% used. Medically and physiologically we already know we don't understand what a large amount of the brain does. Why couldn't it perceive the existance of god? Perhaps the chemical balance in our brain normally prevents it (just like the imbalance in my brain prevents me from concentrating... a task that comes very easily to some). At any rate, sure, it's just an opinion, but there is also no scientific evidence to support that "mind altering" drugs do not, in fact, alter your ability to perceive things.
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