Even if the varnish has been on your boat for years, a cold, damp day can make it appear "cloudy." Normally, the top layer of varnish is clear. That's why, when the sun reflects off the second or even third layer below the top layer, it looks as deep as a pool of water. A cold day or a cold shop can have the same effect as clouds in the sky -- the layers get cold and separate a little more than normal. Where the top and lower layers separate, you have clouds in the varnish.
The "cloudy" part of cloudy varnish is condensation. Even though varnish seals the wood to which it's applied, it's still slightly porous. The surface of the varnish, along with any pockets in the varnish where layers have separated, is cooler than the air around the boat. Moisture will condense out of the air and settle into the varnish. Turn up the heat in your boat storage area and allow the boat to warm up. This allows the surface of the boat -- and the varnish -- to warm up. As it warms, condensation on the surface and below the surface of the varnish will dissipate and the cloudiness may disappear.
When you've tried turning up the heat or towing your boat into sunlight to heat the varnish, in hopes of rectifying the problem, and it hasn't worked, try direct heat. A heat gun, or even a hair dryer, used to heat up the cloudy varnish may resolve the problem. This should work on small spots, but if the clouded varnish is more than a square foot in size, it may be best to wait until a sunny afternoon. Then, you can move the boat out of storage -- where moisture tends to concentrate and condense -- and park it in direct sunlight. If this doesn't resolve the problem to an acceptable degree, you still have one option left.
If the cloudiness defeats your best efforts at resolution, the only option left is to sand and revarnish. You can use a moderately fine sandpaper, something like 220-grit, to rough up the surface of the cloudy area so that two coats of varnish will adhere. Don't use steel wool, though. That will cut through the layers of varnish, not rough it up. You don't even need to break out the palm sander. After you clear the sand away, apply two coats of varnish to the surface.