I think people try to W Heimers turrets too much and take herass for that, which doesnt work at all. Actually, Syndra counters him because she flat out oneshots him all the time lel.
She's a counter to him, but it's because of her burst and not because she is able to reposition turrets. Though being able to throw his ult turret into your tower so it dies quickly is great, or even repositioning it so that it's much less effective. getting two balls out and stunning heimer basically makes it super easy to one shot heimer with your ult, and with Some cdr and mana regen, harrassing the crap out of him is easy and very effective, and since her ult is on a fairly short CD it's easy to see why she wins this matchup.
Now go against a good lux who will pop all 3 of your turrets with her E+passive and ignore your harass.
Just because she can throw a turret doesn't counter him. It costs her a good bit of mana that is better spent on harass to counter him.
Reason she has a lower win rate vs him is that people go in thinking she's a counter and expect an easy game. But end up being wrong. And Syndra has a higher learning curve overall.
If both are decent and equally skilled. Syndra does have the upper hand. But not by much.