One of the main flaws people complain about in Reach is that there are no MAC guns in orbit to shoot down the LNoS (the ship, not the level) in the level of the same name.
However, in TFoR, don’t they say there are only like 15-20 MACs in total around Reach? Now, Reach is a big planet, and about 20 guns is probably just big enough to form a decent defense grid. The average orbital MAC looks to be about maybe 1 km from top to bottom at most. The LNoS is a big -Yoink- ship (19 km). The reason they didn’t use the MAC cannons is because most likely they didn’t know if it would actually destroy the ship before it could counter attack and they probably didn’t want to risk -Yoink!- off the LNoS any more. The slipspace bomb, on the other hand, was almost certain to destroy or at least seriously disable the ship. Losing a frigate and a few fighters is a lot better than losing a whole MAC platform because they were stupid and fired at the ship without killing it.
Also, it is possible that the level actually takes place much farther away than it appears, and it is out of range of the MACs, or the Covenant disabled the orbital guns in the area with an EMP or by disabling the generator on the ground. As for not being able to see them, I doubt a MAC gun would look any larger than a tiny speck from the distance you are at from Reach in that level.