Extended vs. short shaft

I'm replacing a normal sized Nissan 5HP motor with
an extended shaft 15HP Evenrude.
The boat is 12' aluminum.
the new motor will be about 6" lower unless I add some attachment.
Should I expect any problems besides avoiding shallow water?

 

A slightly smaller top speed than with a shorter shaft. The bow will also tend to rise somewhat more with the new motor, because the weight at transom is doubled and prop thrust lever is longer.
But it's really small things, nothing to worry about imho.

 

The Nissan is probably a short shaft (nominally 15", typically about 16") while the Evinrude is probably a long shaft (nominally 20", typically 21-22").

You'll lose a knot or two of top speed due to the extra 5" of shaft in the water; this section is usually somewhat streamlined but if it's not, you'll lose more. You'll have more bow rise and may need to move your helm position forward (consider a tiller extension if you find the boat tends to run stern-down). And expect a hell of a rooster tail when on plane. But yes, it will work, unlike putting a short shaft on a 20" transom.