I agree monsters above cannon fodder should appropiate defenses (for both too few and too many).
However, fortification on items is a magical effect. As such it won't be something to overcome with physical attacks alone.
A rogue surely can learn the trick, or a bard, but a fighter enhancements gotta require some feat or int or something.
Sunder is probably not enough, something like AA's force arrows would make sense.
See
http://www.d20srd.org/srd/magicItems...#fortification
"This suit of armor or shield produces a magical force that protects vital areas of the wearer more effectively. "
Not to confuse with the fort of constructs, undead, oozes, etc. they are outright immune.
Having no vital areas there's little to do to them to cause critical damage except bursts and such weapon effects.
(altough burts of damage are supposed to occur on crits, to account to the weapon hitting a vital area)
Apart of all that, the natural counter from PnP was surely targeted dispel on items.
Not sure if it is general but i believe dispel is fairly underused in DDO.
The whole idea seemed to be that monsters should be dead by the time you could throw a debuff.
Let alone a counterspell, yet there's several situations where a counterspell can be used.
(such as spamming of sleet storm before you get break enchantment, preventing ice storms to put off firewalls, etc.)
Also note that saying fort shouldn't be a magic effect is like saying metalline should be a type of metal.