Good thinking. Ultrasonics are used along with process flow, so you feed algae past the the ultrasound output, basically in a small chamber.
Hielscher.com is an example
The same thing for a smaller scale might be built with a
pond fogger, basically an ultrasonic source, inside a small container with an inlet and outlet. Then you would flow the algae through at a controlled rate, basically slow enough for algae cell destruction to take place. $20-$50.
Lab scale ultrasonic cleaners,
like these, might be better for a production system. $200-$400