the whole 'adding bass' thing is a myth. its never done this... not sure where thats coming from, tbh... (like, there isn't a disproportionate increase on the lower end...)
and, it will be quieter too, yes. you've bypassed the internal amplifier. thats all the prosound mod is, a bypass of the amp IC. you loose the boost for headphones but bypass the circuitry where the background noise is introduced to the signal.
(in a couple weeks i'll have a product out that will address all the cons/concerns you've got about the mod)
oh, and about the speaker. it will keep functioning normally unless you change it. if you simply don't want it to work anymore, remove it.
it won't shut off when you stick a plug into the prosound jack, if thats what you're after. you can add a switch and turn it on/off manually. the original headphone jack has an internal switch (its an uncommon jack type) which turns the speaker on/off depending on if something is plugged in to that jack.
I saw something on eBay and he said he made the bass louder (some How 
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