Yes it's a shame not as many foot passengers use the Harwich-Hook Van Holland ferry crossing compared to 15+ years ago. So I can see the reasons for not running the non-stop Boat Trains anymore.
But it is though a nice way to travel between UK and The Netherlands. Getting the train up to Harwich International(although as mentioned the journey nowadays isn't quite as nice as it was compared to when the non-stop Boat Trains were running!), getting on the ferry, having a nice comfortable cabin for a sound nights sleep, then arriving in The Netherlands about 8-ish in the morning, and a short train journey onto your destination. A little more expensive than the cheapest flight prices, but some people find the airport experience a bit stressful nowadays what with all the check-in and security checks, the noise, and large amounts of people about, etc. I'm not as keen on flying as I used to be. There's also the option of going with Megabus, Eurolines, Ouibus, or FlixBus coaches from London Victoria. But chances are you could probably encounter some heavy delays crossing the channel(via ferry or Le Shuttle) due to numerous problems such as stricter border checks, ferry workers going on strike, French lorry drivers blockading Calais, problems with migrants at Calais, etc, etc! Getting the Eurostar and train over to The Netherlands isn't too bad though, but is fairly expensive.
I remember a few times or so getting the Boat Trains between London Liverpool Street and Harwich back in the 90's. Hauled by the superb Class 86's, and lovely non-stop journeys! A shame those days are long gone. Wouldn't expect the Class 86's to be running nowadays of course(if only though!), but if Boat Trains were still going now, Class 90's would probably be used until the brand new high speed trains arrive.
Would be good if at least though could run an evening semi-fast service from London Liverpool Street-Harwich International. With calling points of say Chelmsford, Witham, Colchester, Manningtree, and Harwich International. So wouldn't be a service for the Harwich-Hook Van Holland ferry users only, but also offering a fast service for passengers travelling to Chelmsford, Witham, Colchester, and Manningtree. Also a train that doesn't have 3+2 seating layout. Class 90's would be perfect!