There are definitely separate systems at play. We once had our pre-cruise reservations not appear when we boarded. We were told that the software used by the ships is independent of the website. This is one reason they tell you to check the Viking daily as there may be a delay with what is on the web. The integration between the two systems must be a periodic data update, or even worse, a manual process.
My career is in IT and I’ve worked on plenty of places that have a hodgepodge of off the shelf, custom software, and multiple 3rd party systems. Integration is always a challenge. I suspect they have an integrated off the shelf solution that runs their fleet and everything offshore is totally different. Ironically when we had our extension in Athens, our hotel was hosting a European computer conference for a company that sold ship fleet management software.