Airmar used to have a warning advisory to never have your transom mount or thru-hull T/D powered out of water for longer than something like 90 seconds or maybe a few minutes or damage may occur, and that if you could hear clicking some damage may already have begun as internals may have heated to the point of loosening internals. This ...might... not still apply to most transducers, but now the closest I can find in their FAQ's is this relating to CHIRP t/d's:
http://faq.airmar.com/index.php?action=artikel&cat=1&id=257&artlang=en :
"Marine Transducers
ID #1257
Can I install a transom mount CHIRP transducer as an in-hull or keel mount?
No. The TM265LH/LM transducer is bolted to the outside of the boat on the transom. The active face of the transducer must be exposed to seawater while in operation.
CAUTION
-This transducer is intended as a transom mount only.
-Do not flush/keel mount, fiberglass into the hull, or install inside a yellow tank.
-Active face and ideally sides of this transducer must be in seawater to cool the unit.
-Due to the placement of required heat sinks within the construction, installing this transducer in a way other than intended by the manufacturer could result in the transducer overheating, leading to transducer failure."
Hummingbird and Garmin still reportedly include warnings against having them actived dry.
A lot of people have said they do occasionally activate them dry for longer periods with no noticeable damage , but my impression is such damage may occur over time and manifest in decreased sensitivity that may not be noticed from one use to the next. Personally , I take care to not run them dry.