To give myself an answer:
After setting some debug marks one has to state: Incoming mail is processed for the cut line before decryption.
Very pity!
[7001] [Wed Feb 21 13:11:02 2024] [debug]: ... in sub ProcessEntity (/opt/rt5/local/plugins/RT-Extension-EmailReplyDelimiter/lib/RT/Extension/EmailReplyDelimiter.pm:161)
[7001] [Wed Feb 21 13:11:02 2024] [debug]: EffectiveType: application/pkcs7-mime (/opt/rt5/local/plugins/RT-Extension-EmailReplyDelimiter/lib/RT/Extension/EmailReplyDelimiter.pm:166)
[7001] [Wed Feb 21 13:11:02 2024] [debug]: Depth: 1 (/opt/rt5/local/plugins/RT-Extension-EmailReplyDelimiter/lib/RT/Extension/EmailReplyDelimiter.pm:173)
[7001] [Wed Feb 21 13:11:02 2024] [debug]: Message encrypted for user@example.com (/opt/rt5/sbin/../lib/RT/Crypt/SMIME.pm:691)
I don’t know if there is a possible hook location for manipulating the mail content after decryption. But maybe there is the possibility to manipulate the view? One could just reduce the Body of each transaction shown from the beginning to the first occurence of a member of $EmailReplyDelimiters.