it should not be a problem, but it might complicate the management of your system later.
the file /etc/init.d/weewx *should* be ignored, since your system uses systemd.
the file /etc/systemd/system/weewx.service will override the systemd unit that was installed by 5.0.2 at /usr/lib/systemd/system/weewx.service
that may or may not be what you want.
i would suggest that you stop weewx, move aside both files, then start weewx. something like this:
sudo systemctl stop weewx
sudo mv /etc/init.d/weewx ~/weewx.rc-old
sudo mv /etc/systemd/system/weewx.service ~/weewx.service-old
sudo systemctl daemon-reload
sudo systemctl start weewx
if there are changes in the old systemd unit that you want to keep, then apply them using the .d pattern for overriding a systemd unit. or just leave the /etc/systemd/system/weewx.service file in place.
m