I don't know if those are factory, since I have never had a later Mercury (post '51) engine for comparison. I notice the engine has a Rochester 2G carburetor which is obviously not stock. Whoever swapped the carb probably added them in an attempt to get the automatic choke (which most 2G's had) to work. Though it seems counter-intuitive, 2G's work best on these old Fords when mounted backwards. It looked like someone tried it the regular way first, then decided it would work best backwards and turned the carb around, thus the fittings on both sides. If you're lucky, they are probably tapped 1/8" NPT and can just be plugged, as they serve no purpose since the carburetor seems to have a manual choke on it now.
I run 2G's on a couple of engines and I think I can add a little to your knowledge base. The engine seems to be a '52 or '53 Merc ("EAC" heads). Even though the Merc manifold has larger throttle bores than a Ford manifold, they are still smaller than those on the carburetor. When I use a 2G on a Merc manifold, I have a fixture that allows me to bore the manifold to match the 2G throttle bore all the way down. I have seen them where the manifold was "bell-mouthed", which while not the ideal way to do it, is better than doing nothing. I have only done these conversions on the earlier Merc manifolds, and on those, the automatic choke linkage is easy as pie, both with the integral and "divorced" choke versions. I have no experience with the later manifolds so all I can say is that the manifold does not have the provisions for the choke stove like the earlier ones. If the choke works, you can probably use it. Normally, a manual choke pulls the wrong way, but it looks like whoever put it on made a new lever on the choke that works properly.