I think the reason that the ships have drifted from their specializations is due to two factors: perceived usefulness, and team-play.
The first issue, perceived usefulness, is due to the skill required to use some tactics rather then others: while most pilots can easily grasp and execute a pyra's headlong charge, the careful maneuvers required by a squid are more difficult to learn, and thus the ship seems weaker, as a larger portion of users have difficulty. This is also seen in several weapons, with the lumberjack and minotaur being prime examples of this perceived weakness: while they are just as deadly as a hwatcha in the right hands, they lack the simplicity of the "OP Liongun".
The second issue of that of team-play. Some ships' specializations are best used with allies: a squid's harassment will be most useful when distracting/weakening the enemy as a more powerful, yet vulnerable ship (such as a spire) uses it to close and engage: the key idea of specializations is to be better in one area at the expense of another, and in proper team play, that weaker area will be filled by a teammate strong in it. However, this doesn't hold up so well when dropped in a lobby with an unhelpful "Ally". This is also seen in the gun examples: while the minotaur is quite powerful in disrupting the enemy, it cannot get a kill by itself, and as such, is seen to be weaker then guns which do not require coordination; the flak also has/had this issue.
Combined, these issues make some ships seem much weaker then they actually are, thus leading to buffs/nerfs that lessen the weaknesses that defined their specialization.
