Sea levels haven't risen all that much - 8 inches in the last 150 years says one reference. There are other options which are more probable. If it was a volcanic island then the top could be easily eroded. Consider the island of Ferdinandea, off the coast of Italy. "At its maximum (in July and August 1831), it was 4,800 m (15,700 ft) in circumference and 63 m (207 ft) in height." while by January 1832 it had eroded to below sea level. Surtsey is another example, this off the coast of Iceland, and Kavachi is a third, this in the Solomon Islands.
If this were the case then depth soundings would easily identify a submerged volcano, even if it were 100m below the surface. A simple visual fly-by wouldn't.