If it is shooting Kinetic weapons, there's the Yamato's strong point. Anything based on atomic structure de-compilation, such as a particle beam, would render almost any battle to the person who got the shot off first.
I only saw Macross (that is 1 of the 3 anime that was re-cut and dubbed for Robotech), but yeah I'm with Zathros this one.
The SDF Macross is much bigger (It has a small city in it for example), has a barrier system etc. so without the the "big guns" it would win.
But Yamato's main cannon destroyed a small continental landmass, and Macross's one destroyed Zentradi super dreadnaughts, so yeah whoever shoots its big gun first probably wins.
Edit: Oh and I don't know if it survived to Robotech, but in Macross they had "Reaction" warheads, that they could employ from valkyrie vari-fighters or missiles, and those are basicallly overpowered nukes, with a full aircraft carrier complement of valkyries to deploy those, if they have time to launch before Yamato shoots, it's a good bet it will be a double KO