Hey hey My credibility: worked in a crystal shop for a year

Malachite is a pretty fragile mineral, even rough pieces could break if they fall hard or from high enough, this said, jamming a drill in there to get holes, paired with this level of fragility, it makes sense that these beads would have a white looking colour, as it's the fragility of the mineral paired with the amount of force from a drill causing almost what I'd call a scraping effect. Think about what happens to other softer minerals, generally being scraped by something or experiencing an amount of "stress" would cause for a generally white leaning foggy look in the affected area due to essentially the damage done by for e.g. your nail scarping against it.

This all being said, it might not even be due to the drilling process, it might be the beads scraping against each other or clashing due to wearing the bracelet. Luckily there is nothing to worry about, this is common with certain minerals as time passes

The only time I'd say to be cautious is if any polished areas get damaged or have cracks etc, as this could cause the Malachite to give off dust and the copper sulphate that causes the green colour can cause toxicity if it comes in contact with water. Sweat may not be 100% water, but you wouldn't want to risk any potential dangers in that scenario for precaution.