It's trivial to get a new ip address, takes mere moments, but getting a new phone number is much more work, and also capital intensive. This puts a massive barrier that only gets more effective over the years (as an increasing number of telephone numbers are Maplestory M Mesos) against bot accounts. However, it does not hamper legitimate gamers at all (because, honestly, in case you've got a computer which could run MS you have access to a phone of some kind).
I understand there are some disadvantages, but I do not think they're large enough to justify not implementing this system. The biggest drawback I can see is that a bot/meso farmer uses your phone number and gets it banned before you attempt to make your account.
In that case, there might be a fairly intensive approach to clear a telephone number (it would need to be intensive to be an effective ban). Either that or you are out of buy Maple Mobile Mesos, but the odds of that happening anyway are slim to none to start with.
Additionally, nexonNA could automatically ban phone numbers from all countries outside of the serviced countries, thus making it harder for chinese meso farmers to operate (they would require a large supply of American/canadian phone numbers and corresponding telephones available to make additional bots).