no you do not drill all the way through, that is why you drill from the back, you only drillout the hole on the backside of the bridge. I would not recomend this on an Alloy frome
why do you want to change your brakes? unless they are very lowend brakes (but on an Alloy bike I doubt that) a good cleaning of the calipers, new pads and cable and good cleaning of the rim with some emery cloth then alcohol should really improve braking
sometimes you can find good quality older nutted brakes on ebay. I believe Tektro and DiaCompe both still make nutted brakes. make sure you get the correct 'reach'. the distance from the mounting bolt to the center of the area where the pad bolts on. most better quality brakes have this stamped on the back.
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“One morning you wake up, the girl is gone, the bikes are gone, all that's left behind is a pair of old tires and a tube of tubular glue, all squeezed out"
Sugar "Kane" Kowalczyk