You are right. I still did have some old packages installed. I checked them all 
manually and now have the following versions installed.

root@traxotic [/var/lib/opendnssec/signconf]$ dpkg-query -l | grep opendnssec
ii  opendnssec                      1:2.1.3-0.2                    all          
dependency package to install full OpenDNSSEC suite
ii  opendnssec-common               1:2.1.3-0.2                    all          
common configuration files for OpenDNSSEC suite
ii  opendnssec-enforcer             1:2.1.3-0.2                    all          
tool to prepare DNSSEC keys (common package)
ii  opendnssec-enforcer-mysql       1:2.1.3-0.2                    amd64        
tool to prepare DNSSEC keys (MySQL backend)
ii  opendnssec-signer               1:2.1.3-0.2                    amd64        
daemon to sign DNS zone files periodically
root@traxotic [/var/lib/opendnssec/signconf]$ dpkg-query -l | grep softhsm
ii  libsofthsm2                     2.2.0-3.1                      amd64        
cryptographic store accessible through a PKCS #11
ii  softhsm                         2.2.0-3.1                      all          
cryptographic store accessible through a PKCS #11 (dummy)
ii  softhsm2                        2.2.0-3.1                      amd64        
cryptographic store accessible through a PKCS #11
ii  softhsm2-common                 2.2.0-3.1                      amd64        
cryptographic store accessible through a PKCS #11

The 2006 DB error is now gone.
The signconf files have been updated.
The zone files have been updated.
The queue actually reports 7 tasks, including: "On Tue Nov 14 14:36:34 2017 I 
will enforce zone dennisbaaten.com"

I'm quite optimistic at this moment. Output of commands seems logical again.

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