Can day cruise boats operate in hi and lo Rhine water

I don't think Viking boats are larger, maybe longer and less maneuverable that KD boats, which are good sized. Water conditions are temporary. I have not heard about event problems, but could be given heavy winter rains. I know the Seine in France is a problem. Heck, the Ohio River is a problem right now as well as rivers in Illinois.
And don't stay in Koblenz. Stay somewhere like Boppard, St Goar, or Bacharach. Much smaller and nicer IMO.

It's not at the discretion of the shipping companies whether their boats will sail or not. If the federal waterway authority stops the traffic because of high tides nobody sails.

Anyway, september is not a month in which one usually expects high or low water.

High water stops boats because they can't get under some of the older and lower bridges.
Low water stops boats because the risk running aground.
Either of these events last a number of days, and follow periods of above or below average rainfall higher up the rivers.

So smaller boats with less "draft" or which are lower can travel when bigger can't. Upstream from Koblenz in the Rhine Gorge section, there are no bridges. A hotel boat may be stuck in a different section of the river, but locally near Koblenz there could be no restriction.

So yes, it may be possible for the local boats to run when the hotel boats can't. But you can't predict high or low, depends on the weather. Just go to Koblenz, you wil probably be OK.

Occasionally if the water level is too high, it covers up the docks as well as the access roads. This does not happen very often though.

There are a few bridges at Koblenz (several highway, one rail). Up the river (SW) from there there are no bridges until almost Mainz. So high water should not be a problem, unless, as Jo indicates, the water covers the land end of the bridge to the floating docks for the boats.