V,
Areas with a high magnetic deviation can certainly cause problems with magnetometer surveys. But depending on the mag you are using and the software, you should be able to sort out deviations based on geomagnetic anomalies. A ferrous object will still give a noticeable trough and peak, where as localised deviations will give just a rise in the reading. Typically this rise will be quite noticeable and can be mistaken for a target. But good software and fine tuning the mag will eliminate these false targets.
The use of a gradiometer will still detect these rises and has no significant effect on the readings. The setup Brad is talking about is basically three cesium mags that still function individually but the software will perform the gradiometer calculations to determine if a target is to port or starboard or directly beneath the boat. The cesium mags are super sensitive and can detect a nail or spike at 30'. With this super sensitivity it also makes pinpointing a little tougher. Thus the gradiometer setup.
There are some other factors that need to be determined when performing a mag survey. One is the size of the object you are wanting to detect. This can have an effect on lane spacing as well as what you would expect to see in a deviation. I would expect that if you have an area of magnetic rock it could likely disguise small ferrous objects, but cannon and anchors should still give a clear peak and trough.
Robert in SC