[Commonizer] Don't filter out @Deprecated non-top-level functions

^KMM-238

native/commonizer/testData/functionCommonization/specifics/commonized/common/package_root.kt

@@ -16,3 +16,8 @@ expect fun externalFunction2()
 
 expect inline fun inlineFunction1() {}
 expect fun inlineFunction2() {}
+
+expect class Holder() {
+    expect fun deprecatedFunction1()
+    expect fun nonDeprecatedFunction1()
+}