I'm conflicted on this one.
On one hand, people often make the mistake of thinking of "college graduates" (or, in this case, "PhD holders") as a similar group across time. A college graduate in the 1950s was more analogous to "upper-middle class, White man" than a "college graduate" today, and it is therefore less of a surprise that the group was solidly Republican. On a similar note, I once saw that Romney and Obama practically tied among WHITE postgraduates, leading me to believe that this group in the past was indeed fairly Republican.
On the other hand, I think people very much underrate the "intellectualism" strain that has always been present in the Democratic Party all the way back to Jefferson to Wilson to today. Just because the GOP was winning the upper classes doesn't mean there wasn't a subset of that group that has always been present in the Democratic coalition, and PhD holders would be the exact type I would imagine. A relevant quote by author H.P. Lovecraft on the Republican Party, made well before the "New Deal Era" had really taken shape:
"As for the Republicans -- how can one regard seriously a frightened, greedy, nostalgic huddle of tradesmen and lucky idlers who shut their eyes to history and science, steel their emotions against decent human sympathy, cling to sordid and provincial ideals exalting sheer acquisitiveness and condoning artificial hardship for the non-materially-shrewd, dwell smugly and sentimentally in a distorted dream-cosmos of outmoded phrases and principles and attitudes based on the bygone agricultural-handicraft world, and revel in (consciously or unconsciously) mendacious assumptions (such as the notion that real liberty is synonymous with the single detail of unrestricted economic license or that a rational planning of resource-distribution would contravene some vague and mystical 'American heritage'...) utterly contrary to fact and without the slightest foundation in human experience? Intellectually, the Republican idea deserves the tolerance and respect one gives to the dead."
It doesn't sound all that different from how your more "intellectually minded" Democrats talk about the GOP today. I think there has always been at least a subset of Democrats who saw the GOP as the "selfish and stupid party," lol.
In order to make a more informed guess, I think I would need to know how many Americans had "PhDs" at each point in our history, but I would imagine that by the 1930s, many PhD holders were voting Democratic, and before that it was still a split group, POSSIBLY leaning Republican simply due to the fact that in order to have a PhD, you had to most likely be wealthy, White and WASPy (but with some of the more vocal "intellectualists" perhaps being more liberal).
This is a great point. Lovecraft is an interesting case, however, because his shift to the political left occurred fairly late in his life mostly as a consequence of the Depression and the failure of orthodox economic policy to alleviate it. Before that, his fairly elite WASP background as well as Social Darwinist and Anglophilic inclinations led him to support the Republican Party (but also sympathize with the Confederacy!) and espouse nativist and aristocratic views in politics. I think at least one observer argued that FDR's similarly elite Yankee background helped ease Lovecraft's own political transition. It seems to me that while intellectuals before the New Deal often did have progressive views, it was often of an elite, anti-democratic kind and generally associated with the Republican Party rather than the Democrats. For example, there certainly wasn't much intellectual sympathy for William Jennings Bryan.