I use the time Shulk is in shield to pile on the damage. Shulk is very easy to punish in this form. I go for a grab before the art wears off, and I hold him until it does. Then I uthrow.
There are no SB punishes on a good zoning Yoshi. His up B always props him up just high enough that he glides over it. A good Yoshi can consistently do this on reaction.
You're supposed to throw Shadow Ball on reaction to his jump right when you expect him to throw an aerial. If you think he's not going for an aerial and instead will go for the "dodge" then just F-Air him.
Yoshi has no aerial that ends before frame 30 (the time it would take Shadow Ball to reach him) so it's all about how scared he is to get hit by the ball. It's not "punishing" him per say, it's more of an understanding what move he's about to do. If it's a defensive playstyle as you say it doesn't matter if you lose the SB as you can charge it again.
Also you can punish a landing F-Air with Shadow Ball. If you see Yoshi do Full Hop F-Air he's probably either going to land with N-Air or another F-Air. Both of those landings Shadow Ball can catch, if you think he's going for the empty jump into Double Jump/Egg Throw as soon as he sees Shadow Ball then just F-Air him.
I know this all sounds easier in theory than it is in practice, but you should just go for the safer options. Yoshi playing defensively and not going in allows you to opt for better spacing and Shadow Balls which are unpunisheable even if you miss. You only have to worry of being on point with your zoning ability and wary of Yoshi's Egg Throw.
I did pile a lot of damage on Shulk but he doesn't die until 190% from U-Smash and 230% from U-Throw (no rage). Also a good Shulk that sees his timer about to run out will understand that you will try and go for a kill, cancel shield and go into a "kiting" monado as soon as he sees you go aggressive.
I mean those are good tips, but those are both of the things I was already doing in my match. This Shulk understood that as long as he stayed away from me during the 8 second Monado timer once he was in Shield he basically had 1 extra stock. The rage he had also completely negated Shield Monado's damage/KB decrease. He literally killed me at 70% from an D-Smash from mid stage while on Shield Stance and killed me at like 50-60% from an U-Smash (Halberd though) also in Shield Stance. It's kind of hard to deal with racking damage when I have to rack 200%+ damage and he only has to get me to 50% with 4 or 5 hits.
There has to be an easier solution than just: "kite him and rack up damage slowly". I guess I was already told to try and go for combos since his weight allows for combos that wouldn't be possible. I have to admit when he was in Shield mode I actually went into heavy spacing/zoning. Utilizing D-Tilt, BSBs, Grabs, Rolls and Teleports to a major extent. I kept beating him by far at the zoning game, I always had him at 160% when I was at 60%, but that 60% is enough for him to kill me, while 160% is not enough for me to kill him.
I didn't think of just treating him as if he was at 0% and comboing him anew, maybe that will make the damage racking much easier. I will try doing that next time (Plus I also dislike going for the heavy camping Mewtwo style of play, it's just not my style).
Note that I don't think Shulk is hard. I was winning by a big margin 4 of the 5 games. It's just that I was putting in way too much effort vs how little effort Shulk actually had to do. The only "good play" he did in our matches was that last U-Smash he got which he "read me" pretty well. I am still salty about that U-Smash because I rolled by mistake. I had already rolled 3 times to get past him and I thought: "He'll expect a roll, so I'll just jump out of my shield (which I was currently holding) and teleport past him", apparently the jump didn't register so I ended up rolling and he read it since I had already rolled 3 times by then. He was at 160% too, so close to 200% where I could just go for the U-Throw since it was Halberd.
This was losers semis too and I would have faced a Falcon that lost to me in friendlies right before the tourney, beat me 3-1 in winners semis (although I SDed at 0% on game 4 and I still managed to get him to last stock, kill % with only one of my stocks) and then lost 2 games to me in friendlies after the tourney. I am confident that there was a good chance I could have beaten the Falcon and gone to Grand Finals (where I know I would have lost, but at least I would have gotten 2nd instead of 4th). So salty, lol.