Hm. Okay, wenn es sonst läuft würde ich das wohl so lassen.
Gut möglich, dass sich das bei kommenden Updates vom js-controller und/oder nodeJS zurechtruckelt.

pi@second-device:/opt/iobroker $ sudo -H -u iobroker npm install iobroker.js-controller
npm WARN deprecated request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142

> iobroker.js-controller@3.1.6 preinstall /opt/iobroker/node_modules/iobroker.js-controller
> node lib/preinstallCheck.js

NPM version: 6.14.8

> iobroker.js-controller@3.1.6 install /opt/iobroker/node_modules/iobroker.js-controller
> node iobroker.js setup first

Existing earlier generated certificate is invalid (too old, validity longer then 345 days or keylength too short). Generating new Certificate!
object system.certificates updated
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@~2.1.2 (node_modules/chokidar/node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@2.1.3: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"arm"})
npm WARN winston-daily-rotate-file@1.7.2 requires a peer of winston@2.x but none is installed. You must install peer dependencies yourself.

+ iobroker.js-controller@3.1.6
removed 8 packages, updated 4 packages and moved 2 packages in 35.343s

10 packages are looking for funding
  run `npm fund` for details

pi@second-device:/opt/iobroker $ npm list winston
iobroker.inst@2.0.2 /opt/iobroker
├─┬ iobroker.js-controller@3.1.6
│ ├─┬ prompt@1.0.0
│ │ └── winston@2.1.1
│ └── UNMET PEER DEPENDENCY winston@3.3.3  deduped
└── UNMET PEER DEPENDENCY winston@3.3.3

npm ERR! peer dep missing: winston@2.x, required by winston-daily-rotate-file@1.7.2
npm ERR! peer dep missing: winston@2.x, required by winston-daily-rotate-file@1.7.2

cd /opt/iobroker
npm list winston

Aus Interesse, wieso diesen Befehl? Ist das nicht alles up to date?

pi@second-device:~ $ which nodejs && nodejs -v && which node && node -v && which npm && npm -v && apt policy nodejs
/usr/bin/nodejs
v12.20.0
/usr/bin/node
v12.20.0
/usr/bin/npm
6.14.8
nodejs:
  Installiert:           12.20.0-1nodesource1
  Installationskandidat: 12.20.0-1nodesource1
  Versionstabelle:
 *** 12.20.0-1nodesource1 500
        500 https://deb.nodesource.com/node_12.x stretch/main armhf Packages
        100 /var/lib/dpkg/status
     8.11.1~dfsg-2~bpo9+1 500
        500 http://archive.raspberrypi.org/debian stretch/main armhf Packages
     4.8.2~dfsg-1 500
        500 http://raspbian.raspberrypi.org/raspbian stretch/main armhf Packages

cd /opt/iobroker
sudo -H -u iobroker npm install iobroker.js-controller

pi@second-device:~ $ cd /opt/iobroker
pi@second-device:/opt/iobroker $ iobroker stop
pi@second-device:/opt/iobroker $ npm i winston@latest
npm WARN winston-daily-rotate-file@1.7.2 requires a peer of winston@2.x but none is installed. You must install peer dependencies yourself.

+ winston@3.3.3
added 3 packages from 1 contributor, removed 1 package and updated 2 packages in 23.471s

13 packages are looking for funding
  run `npm fund` for details

pi@second-device:/opt/iobroker $ iobroker fix
library: loaded
Library version=2020-06-12

==========================================================================

    Welcome to the ioBroker installation fixer!
    Script version: 2020-06-15

    You might need to enter your password a couple of times.

==========================================================================


==========================================================================
    Installing prerequisites (1/3)
==========================================================================

Holen:1 http://raspbian.raspberrypi.org/raspbian stretch InRelease [15,0 kB]
Holen:2 http://archive.raspberrypi.org/debian stretch InRelease [25,4 kB]
OK:3 https://deb.nodesource.com/node_12.x stretch InRelease
Es wurden 40,3 kB in 1 s geholt (35,2 kB/s).
Paketlisten werden gelesen... Fertig
Installed gcc-c++

==========================================================================
    Checking ioBroker user and directory permissions (2/3)
==========================================================================

Created /etc/sudoers.d/iobroker
Fixing directory permissions...

==========================================================================
    Checking autostart (3/3)
==========================================================================

Enabling autostart...
Autostart enabled!

==========================================================================

    Your installation was fixed successfully
    Run iobroker start to start ioBroker again!

==========================================================================

pi@second-device:/opt/iobroker $ iobroker start

pi@second-device:~ $ which nodejs && nodejs -v && which node && node -v && which npm && npm -v && apt policy nodejs
/usr/bin/nodejs
v12.20.0
/usr/bin/node
v12.20.0
/usr/bin/npm
6.14.8
nodejs:
  Installiert:           12.20.0-1nodesource1
  Installationskandidat: 12.20.0-1nodesource1
  Versionstabelle:
 *** 12.20.0-1nodesource1 500
        500 https://deb.nodesource.com/node_12.x stretch/main armhf Packages
        100 /var/lib/dpkg/status
     8.11.1~dfsg-2~bpo9+1 500
        500 http://archive.raspberrypi.org/debian stretch/main armhf Packages
     4.8.2~dfsg-1 500
        500 http://raspbian.raspberrypi.org/raspbian stretch/main armhf Packages

pi@second-device:/opt/iobroker $ npm list winston
iobroker.inst@2.0.2 /opt/iobroker
├─┬ iobroker.js-controller@3.1.6
│ ├─┬ prompt@1.0.0
│ │ └── winston@2.1.1
│ └── winston@3.3.3
└── UNMET PEER DEPENDENCY winston@3.3.3

npm ERR! peer dep missing: winston@2.x, required by winston-daily-rotate-file@1.7.2
pi@second-device:/opt/iobroker $ npm list winston-syslog
iobroker.inst@2.0.2 /opt/iobroker
└─┬ iobroker.js-controller@3.1.6
  └── winston-syslog@2.4.4

Zuvor aber wie @Thomas-Braun gerade vermerkte:

pi@second-device:/opt/iobroker $ which nodejs && nodejs -v && which node && node -v && which npm && npm -v && apt policy nodejs
/usr/bin/nodejs
v12.20.0
/usr/bin/node
v12.20.0
/usr/bin/npm
6.14.8
nodejs:
  Installiert:           12.20.0-1nodesource1
  Installationskandidat: 12.20.0-1nodesource1
  Versionstabelle:
 *** 12.20.0-1nodesource1 500
        500 https://deb.nodesource.com/node_12.x stretch/main armhf Packages
        100 /var/lib/dpkg/status
     8.11.1~dfsg-2~bpo9+1 500
        500 http://archive.raspberrypi.org/debian stretch/main armhf Packages
     4.8.2~dfsg-1 500
        500 http://raspbian.raspberrypi.org/raspbian stretch/main armhf Packages

Befehle für das Update

cd /opt/iobroker
iobroker stop
npm i winston@latest
iobroker fix
iobroker start

which nodejs && nodejs -v && which node && node -v && which npm && npm -v && apt policy nodejs