For most of my run-throughs, I ran into her near the forests of Gongaga. Possibly closer to Costa Del Sol... It was definitely after the boat ride, that's for sure. It's been ages since I've done that though. For my later plays, I pick her up near the forests of Junon. Dunno how close those are to the cave area you're talking about (too lazy to look for a map...), but if it's much further, maybe try doing that? But yeah. That's kind of weird that she's not showing up for you.
I like Yuffie. She does have her annoying moments, but I like having her in battle. Her long-range weapons are nice, and I like her limit breaks.
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