Here are a few points highlighting the benefits of each probe. It is up to the user to make an informed decision on what is best for the measurement needs.

Side-looking probes

• Less likely to have the problem of “weak spots” (unless the sampling volume is very close to a side boundary), so they are a little more robust to operate, especially in high flow environments.
• Have higher instrument noise in the vertical than in the horizontal.
• Are well suited for use in wave flumes.
• Have an awful response to flow coming “from behind” the probe.
• Can act as a 2D system in shallow water, if the two beams slanted 65° from the vertical are in air.
• Are more sensitive to the instrument Y velocity (component directed into/away from the center transmitter).
• Because the transmit pulse is typically directed away from the bottom boundary you will be able to measure a bit closer and a bit shallower than you would with the down-looking probe.

Down-looking probes

• The measurement volume can get a few mm closer to the bottom than is possible with the side-looking probes.
• Have a better response in the instrument Z velocity component. 
• Provide redundant measurement of the Z component, which can be useful in data screening.
• Have the lowest noise in the vertical.

Check out the Principles of Operation for an overview of the sampling volumes for these two probes.