As you probably know, some vegetation (like posidonia) has a very high acoustic echo due to biological activity that causes fine bubbles to build up on the vegetation.
The distribution of such vegetation can be mapped on the seafloor using high-frequency sidescan sonar. I found some examples of Posidonia in sidescan sonar imagery on this web page:
http://www.idrogeotop.it/rilievisss.html
You may have to do some spot checks (send a diver down, or ROV with lights and camera) in order to confirm that what you think is vegetation in the sonar image is in fact vegetation.
Sonar will not "see" vegetation that has very low acoustic reflectivity (acoustically invisible), of which there may be many kinds. But that vegetation will not interfere with bathymetry measurements.
Note that there are products for seabed classification, designed to operate with all of the main bathymetric sonars and echo sounders (I believe). These analyze the sonar's echo off the seafloor in order to classify the kind of material present on the seafloor, in real time. Such products could presumably be trained to detect, classify, and map the distribution acoustically reflective vegetation.
See for instance the QTC Seabed classification software:
Such products are designed to discriminate mud from sand, from clay, from silt, etc., but they should be able to classify seafloor vegetation too, especially posidonia, You have to speak with the manufacturer.
For acoustically reflective vegetation, then, you might at least map its distribution (sidescan sonar) or detect its presence in bathymetric sonar (seabed classifier), in order to identify where vegetation may be interfering with bathymetric measurements. Correcting against their interference is more difficult.