Germany's missing Atlantic reconnaissance network

Could flying-boat submarines make the Battle of the Atlantic much harder for the Allies?

No; Germany needed roughly five or six times as many long-range maritime reconnaissance aircraft instead.

Germany needed reliable information about convoy positions across the Atlantic. Many convoys crossed safely because wolf packs were in the wrong place or had left to refuel, even without a special diversion based on codebreaking. A submarine following a convoy on the surface could report its position, but radar-equipped escorts would eventually find and attack it. Several times more Condor-like long-range aircraft are proposed as a better way to locate convoys and direct U-boats.