I doubt the spikes are intended to provide lift: I suspect they are there exclusively to provide an oblique shock to the inlet. As such, they would (for optimum air-compression performance) be aligned with the local flow streamlines. The local flow streamlines will be directed slightly outward from the fuselage at the engine inlets, when looking down from the top (your second image). Also, the aircraft does not fly "level", it flies at some angle-of-attack, the entire fuselage and engine nacelles providing lift. Hence, the spikes are pointed downward with regard to the fuselage (your first image) -- the spikes ARE flying "level" into the wind, it's the fuselage and engine nacelles that are angled upward with regard to the wind. CWatters' video kind-of shows this at about 2:10 -- the engine is pitched slightly nose-up, but the inlet spike is aligned with the inlet flow. Unfortunately, in the video they colored the inlet air to make it look as though the flow direction aligns with the nacelle, which it does not do in normal flight. They did, however, get the oblique shocks aligned correctly near 2:55.
Now, having said that, I should point out that I never worked on the SR-71, nor at Lockheed. But my experience as an engineer is that you start with nice clean theory (my first paragraph), then in testing you learn a lot, and you tweak a lot. So, the inlet spikes MAY provide some lift, and they may (possibly for several reasons) NOT be exactly aligned with the local flow streamlines. But if I were designing the inlet, what I said in the first paragraph would be where I'd begin the design iterations.