Try this instead
expr := Hold[Cos[\[Omega]Hold[Cos[ω t - \[Pi]π/4 + 3 \[Pi]π/4]]
rule := Cos[a_ + b_] :> X[a, b]
ReleaseHold[ReplaceAll[expr, {rule}]]
X[t [Omega], [Pi]/2]
X[t ω, π/2]
In reply to the comment
expr := Hold[Cos[\[Omega]Hold[Cos[ω t - \[Pi]π/4 + 3 \[Pi]π/4]]
rule := Cos[a_] :> (a /. List -> X)
ReleaseHold[ReplaceAll[expr /. Plus -> List, {rule}]]
X[t [Omega], -([Pi]/4), (3 [Pi])/4]
X[t ω, -(π/4), (3 π)/4]
I'm sure there is a simpler way.