Would it be practical that nuclear-powered seaplane (only flying low over the sea) or hovercraft can be an alternative to cargo plane or ship?
There is a long list of other issues as well, but in order to avoid a too long post I stuck to adressing the points you made in the question.
As with most other things this boils down to the economics. If we assume that the technical challenges can be resolved and you're able to build something that fly according to your description, it will still cost a lot to develop and build. But how much does it cost to carry a full load from A to B compared to the other options, and how long does it take?

It may be a competitor to cargo planes or ships.

Ships are great for freight because they carry a lot of stuff at once cheap but slow. Aircraft are great because they go fast and high, and are less impacted by weather, but at a higher cost while carrying less.

The flying height of this aircraft is only one or two hundred meters.

One of the advantages of existing aircraft is that when something go wrong, you can trade altitude for time to troubleshoot. Flying at a few hundred meters means less time to troubleshoot; being powered by a nuclear reactor means that you will need a lot of redundancies to minimize catastrophic system failures. You'll also be more exposed to weather, which will increase the stress on the airframe compared to other aircraft.

Flying only over the sea and can landing on the sea.

This will expose you to more salt water, which will drive both R&amp;D costs to make the aircraft more resistant to corrosion, but it will also increase maintenance costs in the long run.
Landing and taking off from water is harder in bad weather or at night. A land-based plane can usually count on having runway lights available, and a firm surface to land on. A seaplane has neither but will be affected by waves in addition to wind.
This will also limit the routes you can fly, and therefore also the potential customers for this plane.

And the speed is low. It can be safe enough.

Flying slow will make you less able to avoid bad weather; flying around it might not be possible before it overtakes you. While in theory you could be able to land instantly in case of problems if the cruise speed is close enough to the landing speed, you'll still have weather to contend with.
Crashing at 200kph isn't automatically safer than at 800kph. Using nuclear power will limit which countries would allow operations, as one crash would be enough to destroy an entire area.

Container-sized Small Modular Reactor can be under 100 tons.

This is less than the fuel weight of a 747-8F even if you add engines. According to this question electrical engines are likely to weight around twice as much as comparable turbine engines, so with a bit of goodwill and a lot of assumptions we can replace the engines and fuel load of a 747-8F with a reactor and 8 engines.
Even if this were to work, I suspect the maintenance costs would be huge, and you wouldn't really solve a problem. Chances are you'd go slower than existing aircraft but at a higher price and with a less reliable timetable.