The two likely reasons for such deprecation would apply just as well:
1. Updated Baseline Requirements or a programme policy requirement at any of the major root trust stores could forbid this challenge or require it to be substantially modified, obsoleting it in its current form.
2. The BRs don't change but Let's Encrypt finds they need to adjust this particular implementation in a non-compatible way so they deprecate the current challenge.
It can be easier to do DNS challenges, but it can also be very rough, depending on all the moving parts in your system.