I agree, do the test and let us know if it works!
This paper seems to suggest that the JSN-SR04T will work when submerged.
"seems to suggest" is an interesting and appropriate choice of words.
I looked through that thesis and decided that very little of it can be believed.
Figure 4.2 shows extremely noisy and unconvincing depth information in one dimension along X, down to about 70 cm, and the so-called 3D reconstruction is obviously just the 2D data simply repeated along the Y axis.
A much more interesting project is the autonomous lake mapping boat Sea Renderer, which uses the professional Airmar DST800 underwater transducer (cost about $270).
Such a transducer is required for efficient sound energy transfer to water, which has acoustic impedance about 3500 times higher than air.