Hello Steve,
1. In my point of view, depends on your needs. Installing dcm4chee in separated machines let you scale better for your needs, and this strategy let your environment more flexible. But I still prefer do it using docker, that's too much easier to do everything, and let your environment configurable and reproducible in case you need mount the same environment in another location/server.
2. No, the recommendation for Apache Directory studio is just to make your life easier in order to run add ldif files to your LDAP. You don't need desktop environment to run dcm4chee. In your case, you could install Apache Directory studio on your local machine, and connect it to your LDAP server (like a database client -- like mysql-workbench, pgadmin)
I hope it helps you! =)
Abraço!