Back in the original, not only was there no way to tell at glance which walls were bombable but if you ran out of bombs in one of the later dungeons where you simply had to bomb a wall to get any further, TOUGH LUCK. Up against dodongo and out of bombs because you mis-timed your last one? DIE. And if you were low on rupees to buy more bombs, tough again.

In phantom hourglass, if bombing a crack is necessary to advance, not only will there be a massive crack visible, but the DS will actually switch to a cutscene the first time you enter that room specifically highlighting the crack. If that's not enough there will be a huge SIGN nearby telling you why not try a bomb, and in case you had not thought to bring any, there's also a bomb-plant providing an infinite supply in the corner of the room. If I remember right, for the boss that you need arrows to defeat, there's some kind of infinite resupply in the room as well.

P.S. I wonder how many times you need to mention "bomb" on HN to trigger an XKEYSCORE alert?