They do scale. Someone I know was using the TOS Constitution in Commander-level missions. She said it was really, really hard but the weapons had scaled enough to be useful.
I believe the hull scales as well. My lowbie with her Con has 12000 hull, while my almost-LtCmdr has almost 13000 hull.
The phasers, at least, scale well enough to be used at all levels. At 42, my blue phasers do about about 5dps less than my MkX plasmas (phaser and plasma skills maxed). Thus, you're not hurting yourself at all if you decide to keep using them throughout your career.
Now I am beginning to wish I got the gamestop pre-order instead of the Amazon Borg BO. I mean who really see's the borg anyways? She only goes with you into your instanced away missions and offers nothing really special.
I am kinda hoping that Cryptic will eventually put all pre-order bonuses in the C-Store.