The oddity now is that sieve seems to be working when there is no compiled version
It could be that you have actually a compiled sieve script svbin file somewhere else thats referenced in dovecot config perhaps in global, before, after or default and thats the one working otherwise probably your per user and claws mail is working just fine or its your default/global being treated as a per user and auto compiled while it should be already precompiled.
Should I expect a compiled .svbin version to be generated from claws client? Or generated by first run of the sieve server on the user account? Or should I manage the scripts with claws, but log in to the server later to generate the .svbin versions?
It depends on your mail client, if it supports pigeonholes then it can rely on its managesieve server to generate svbin, write to and read sieve scripts. Compiling per user scripts manually doesnt seem to be the right way, I recommend to look for better mail client.
In any event what effect does not having a .svbin version have on typical small installation?
Svbin file its required for global/default sieve script while svbin file for per user its going to be generated by e.g. managesieve during runtime i.e. sieve for per user will not work if pigeonholes fails to generate its svbin.
Typically, principal script i.e. global/default script which every email is going to be sieved through, must be configured in dovecot config and pre compiled in same location with identical name, while the per user i.e. sieve script which have to reference the per user script file beside an active link file symlinking the user script, and its svbin will be dynamically compiled in new email event in pigeonholes powered email server.
Reference https://doc.dovecot.org/configuration_manual/sieve/configuration/#basic-configuration
