Is it a good practice to indicate the desired handling editor when submitting a paper?
I would only do so if you have a very good reason to want a particular editor (or to avoid another one): while there can exist valid such reasons, it could also be a warning sign for editors. For example, if you ask that the editor not be the “usual” editor for your particular subfield, it may be regarded as you trying to avoid careful scrutiny. So, if you are not asked about it, and you don't really care (or trust them to make the right call) (which should be the majority of cases), just don't do it.

Regarding usage: most of the chemistry journals I know allow you to pick your handling editor directly from a list (although availability and workload management might lead to changes after submission), and some journals allow you to pick both preferred and non-preferred editors.