I believe this only happens when the resource is not considered adjacent to the city (i.e. several tiles away from built structures..) If this is the case I do not find it a real issue.. I actually like that when i simply want to build on a resource i can skip clicking the city build button as this is one less click...

Perhaps this is true, as I did move my city an additional square away from the fertile land in order to be slightly closer to some nearby gold mines.  That doesn't address the issue I have with it though.  Why should some buildings be built within the build menu, while others require me to click on the square to build them?  As my zone of influence increases, does this mean I will have to manually scan the surrounding area and click on each individual mine/lost library/horse/forest etc. and hope I haven't missed one around any of my cities?  Shouldn't the build menu be automatically updated when my zone of influence increases and add any additional options for unused specialty tiles that I have the proper research for?

I think the zone of influence and building on any specialty tiles without having to be connected is a great idea, but it should be a bit easier to maintain.  You mention having to do one less click, yes, but I'd rather have one extra click then have to manually scan the map for specialty tiles.  All I'm asking for is to be able to use the city's build menu to perform all building construction within its particular zone of influence.

EDIT: Tested just now and they do show up in the build menu if you have something built in an adjacent square.  They do not show up in the menu if you do not.  I demolished a building next to a gold mine and the option for building the gold mine also disappeared from the city's build menu.  I had to click on the gold mine to build it instead.  I think this is a bug with the new zone of influence system.