Even omnidirectonal mics get somewhat directional at high frequencies. The extent to which that happens, and the shape of that pattern is determined by the design of the microphone. Generally the smaller the mic is, the higher in frequency it will retain it's omnidirectionality. It's enough to hear a difference with many omnis.
In general its a good idea to point the mics at the source if you want to get those highest frequencies on your recording. Sometimes people point them straight up for measurement purposes so the respose is uniform from all horizontal directions, or to pick up less of the highest frequencies from the source if that's what they want.
The virtual microphone configuration programs usually model an ideal omni, which doesn't take that aspect into account. It would be difficult to display the relavant data anyway if they did, since it varies by model and doesn't make a difference for most of the audible frequency range.
So in terms of Stereo Recording Angle it doesn't really matter how you point the omnis, only how much you space them. How you point them is more of a timbre / high-frequency response thing.