I have been using Nethserver for quite a while now, i love it and love the community behind.
Funny enought i have been using it only for advanced projects, softwares and scenarios, mostly nase don Howtos, wiki and modules that are available on the platform.
q: which is the best and easiest way to host standard web applications onto the platform,
this is considering, use of database, MYSQL or PGsql.
use on a fully qualified domain and use on a subdomain.
these are software like matomo, mailwiz, etc. which can be hosted on normal shared hosting plans.
Use the virtualhost module for managing your sites. This way you get separate (sub)domains/webspaces and you may use different PHP versions and certs for your sites. Files may be uploaded with (S)FTP.
When I remove a vhost from server manager it’s completely removed including /var/lib/nethserver/vhost/<vhostdir>/
When I recreate it it’s recreated without problems.