Run up shield is an inherently good option against Yoshi, I agree. If you truly are aware of your opponents' habits, though, you should be able to get around this. Have you considered just poking them with Dtilt as they run at you or something? You'll whittle their shield down eventually. If they're continuously picking defensive options you can bait one out and punish. What you're describing is hard to accurately address without vids, and without them all I can really say is "try to be better than them".
If spot dodge/OoS Retreating Nair are their options of choice, you should pick things that beat those options. Delayed SH Aerials work. Fair has long range, you could space that. SHAD > Nair or something could also be the ticket.
You can also SH away as they run at you then Egg Toss them. It'll whittle their shield down until they eventually stop, I imagine.
This is a bit harder to deal with due to the lack of a good pivot grab. You could try preempting them and hitting them before they'd expect to need to shield. Even if they do shield, rushing them with a Dair could work to pop the shield or poke them, setting you up?
CalebGamer14
Please don't double post. Use the edit function to add more to your last post, rather than posting two in a row.