i dont think that this is true anymore, there are plenty of warnings on new motherboards not to plug in 5v agp cards, especially with the latest crop of nforce motherboards.
check out the asus a7n8x spec for agp
link
it works for 1.5v agp only.
most motherboard manufacturers put in some protection so that the system will not boot with the wrong voltage agp card in the slot, and usually a red led on the mb labeled "agp protect" comes on.
it is this way for the asus p4pe, a7n8x as well as the shuttle sn42g. these are the only mb that i have experience with in this respect.
edit*********
oops, my bad. you want to put a newer video card into an older board. that's usually cool. it's the other way with an older video card into a newer agp slot that can give problems. i'll leave this post here rather than erase it so people can laugh at me for not reading the question right.