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Generally speaking, especially in the case of specific complex structures like sidesystems, shaping will usually have some kind of an impact on the entire system. However, some systems may not see it that way, because shaping is such an overarching process that saying "everyone in this sidesystem is affected by shaping" sounds like it's saying "everyone in this sidesystem is shaped in terms of origins or functions", which is not always true.
A collective identity, in terms of a system, is basically something that the entire system feels they are, even if individually not everyone in the system is. This can include, say, having a collective gender because it's the one you present as having in real life.
In terms of something like forcishaping, what it would mean for a system to collectively identify as shaped could include, for example, a system that is forcigenic and forcibased and thus collectively affected by shaping, but not all headmates in the system are forcimates, and it's hard to make generalizations about in what way shaping affects the entire system.
It could also refer to a subsystem that came to exist through programming but is not really subject to programming triggers now, and where not all headmates currently existing in the subsystem exist due to programming or ever had programming.