0. You need to provide a lot
more proof for your statements. The effectiveness of anything cannot be proved by only analyzing the tech tree and weapon modifiers, actual strength of the items needs to be taken into account. The same statements were true in 3.1.0, yet cannons were known to be barely useful.
1. Mortars and howitzers are not part of the cannon branch; they branch away very early (after cannon damage mk1), they have a separate set of upgrades to pursue. On the contrary, MRAs and ripples (and later seraphs and archangels) use the same set of upgrades as other rockets and missiles (minipods-lancers-TKs and later scourges, respectively), and you also have an ultimate weapon against buildings in the rocket branch, namely bunker buster, also available for free.
2. AA weapons are available in rocket branch as well, and i cannot say that the free cannon branch AA is better than the free rocket branch AA, specially when it comes to the excellent use of Sunburst as air-to-air. Also, rocket branch provides a nice T3 AA kit, which railguns fail to provide. And the latter is actually very important, because T3 VTOLs are a major threat (slightly smoothed out by the universal availability of the Stormbringer).
3. Rail guns are penetrating, but seraphs are indirect-always-hit (where indirect provides hitting stuff that cannot see you and fire back, and also perfect unblockable fire concentration) with very nice DPS, which makes the latter kick ass even of railguns on certain terrains (assuming you do play maps with terrain, otherwise balance is undefined and unsupported).
4. Cannons are not effective against cyborgs, as in you cannot survive with pure cannons against pure cyborgs. A cyborg-intensive mix is the right counter against cannons, at least on the early phase: not only they win in direct combat, but also harass effectively. You would just need less machineguns in the mix, but you cannot go on without having at least some. At around heavy cannon and twin assault cannon timing, cyborgs become less effective in general, so you'd probably manage somehow, but you won't survive till then unless you have some AP weapon around. Mortars might be good against cyborgs, but MRAs are even more so, as they allow cobra hover hit-and-run against most cyborgs due both speed and range being better. Also, at HC/TAC phase, your biggest problem would be dealing with tracked tanks, when you suddenly find out that you have no good weapon at all (!) against them, to compensate their huge HP/$ boost.