It depends very much on how you clean them, and why.
Parts that were covered in mud or excrement will have lower value after that regardless of how you clean them, but I suggest it's not the cleaning that is the cause. Similarly for parts exposed to cigarette smoke or other toxic substances. If you check Bricklink, for example, many sellers of second hard parts say "smokefree household" as an advertising claim.
Careful cleaning with things that don't damage the Lego would normally increase the value, but not enough to cover the cost of doing it (otherwise more online sellers would say "all parts washed before sale"). Most Lego is kept pretty clean, except for smoke damage as noted above.
I have preciously sold Lego that I bought in a big, foul-smelling bin after washing it to remove the smell. The smell was slight rancid, slightly just "house that is never cleaned" musty/mouldy. So I used laundry detergent and warm water, soaking and agitating over a day or so, then rinsed a couple of times and dried in the shade. The smell disappeared, I sold most of the bricks (I bought the lot for some specific parts). I removed all the transparent parts before cleaning, and carefully hand-washed each transparent part specifically to avoid visible scratches. But the scratches from the general washing seem likely to be less than the scratches from normal keeping Lego in a big bin and carrying that around. I didn't see any obvious new damage, at least.
I suspect but have not tried that machine washing would cause more damage. Bag washing in a dishwasher or washing machine will involve more agitation and possibly hotter water than the hand-washing I've done. If I was going to do this I'd try it first on a bag of low-value Lego. AFOL groups often have a supply of very low-value bricks from people who regularly buy bulk lots of second hand Lego, so it would be worth asking around for how they clean it or whether they'd be willing to donate some bricks for your experiments.
I have heard of people deliberately using reactive chemicals to "clean" bricks in a damaging way. Normally this is done with old white Lego that has yellowed with age. Oxygen free radical cleaners will restore the whiteness, but make the Lego brittle. Doing that would definitely lower the value of the Lego.
I am assuming here that everyone involved is honest - obviously if you do use harsh cleaners but don't tell buyers that's not going to affect the value until the buyers discover the problem, and then only if they have some way of telling future buyers about your actions.