First, I think you're absolutely right in identifying a systemic problem with the organization. Identifying and developing position players has been a pressing issue for almost two decades, and it isn't even close to receding just because Manny Machado
appears to be a stud and Johnathan Schoop is a promising prospect who's made his way onto some top 100 lists.
However, I think you mistake a few things.
What matters, at every position, is overall value. Whether a guy presents that value through a high OBP or SLG or defense or baserunning is ultimately immaterial, so long as their strengths are more than enough to make up for their weaknesses so that they can still provide overall positive value.
So, in the context of Johnathan Schoop, that means whether or not he hits a lot of singles or hits for a lot of power ultimately doesn't matter very much. What's important is that his overall value is that of an above average 2B. Is he an above average 2B? I have no idea. He hasn't even played in AAA yet, is still very young, and oh by the way I've only seen him play a handful of times, so what the hell do I know? But even still, the means of producing positive value is far less important to the basic question: can he he provide positive value? According to many scouts, and apparently in the eyes of the organization, there's a good chance that he can, though the jury's out on whether that's at 2B (where he'd presumably be an above average bat with hopefully average defense) or at 3B (where he'd probably be closer to an average bat with above averagish defense). Or maybe he won't be a starting caliber player at all! We don't know. That's the nature of prospects. But that doesn't mean they don't figure into your long-term plans (which should always be written in pencil anyway).
Hardy's under contract for two more years. Maybe he stays at SS and Machado stays at 3B and the left side is set for the next two years, and the only in-house hope for a good 2B is Schoop, who may or may not be capable of filling the need. Maybe Hardy moves to 2B and Machado moves to SS, the middle of the infield is set for the next two years, and the only in-house option at 3B is also Schoop, who once again may or may not be capable of filling the need. Or maybe Hardy gets traded, either for something that fills a need at 3B or 2B or for something else entirely, and the org looks to Schoop or a new acquisition to fill in one of those two positions, with all the necessary understanding that no prospect is a sure thing. Or maybe Hardy sticks around, either at SS or 2B, and Schoop is packaged in a trade of some sort for a MLB-ready 2B or 3B who comes in to fill the void.
And amidst all this, you've got the ever-present option of adding veterans on managable, short-term contracts who can always plug a hole for a short period while having a good chance of providing positive value. Guys like Kelly Johnson are always out there, and can always offer a good chance at providing league average or greater production at a small cost.