Single casino chip collecting is similar to collecting coins or baseball cards or stamps. It just so happens that casino chips are great to use as poker chips, too. As a collector of singles, if the chip is extremely rare, than I'd rather have a cancelled chip vs not at all.
Another factor is price, where a very rare chip could be thousands, but the drilled version is way more affordable. It's kind of like a Michael Jordan rookie card graded as a 8 vs 9 vs 10. Huge price difference. The difference in the chip world is that a very rare chip can have a population 1 or 2 or 10 total known (any condition) vs thousands of MJ rookie cards (though the demand for MJ cards are way higher!)
Making them into key chains is really why many of them are drilled, as they were made into key chains to sell in the casino's souvenir shops, like the one from the Flamingo below.
Here are a few of my drilled examples