My understanding is that decompositions for Latin scripts was just natural typewriter-style constructions, while precompositions for Latin scripts was also natural to simplify table-driven transcoding between Unicode and ISO-8859.
Similar considerations probably applied in the case of Hiragana (I'm guessing) and other scripts.
Besides, combining marks (decomposition) allow for creating new glyphs based on existing ones even where Unicode does not define them.
Once two or more ways existed to write any given glyph the canonical equivalence problem immediately arose, and the UC was aware of it immediately, thus we get two basic NFs (NFD, NFC).
When it comes to the semantics of glyphs, whatever the UC intended is one thing, but how natural language evolves to use those glyphs is another. So to some degree what the UC intended is a footnote, and what matters is how people use Unicode.