I don't have a save handy (also at work) but I routinely declare war in the fashion described by Protaxis, and take no reputation hits whatsoever. Sometimes attitudes are negatively affected by my aggressive behavior against my neighbor, but my reputation remains unscathed.
The only way I know of to confirm reputation status is seek (1) an RoP with a civ, or (2) seek to buy an asset on a per-turn basis, and watch the reaction of your advisor. Attacking with units in territory (but not moving into territory after a declaration during the same turn) makes an RoP much more difficult to get, and sometimes impossible (Advisor: "They would never accept this deal" -- if actually proposing it anyway, the civ will usually respond with a reference to your treachery against XYZ civ). Attacking with an active RoP in place will always (in my experience) make an RoP with others impossible for some time. Breaking an active trade deal will generate "never accept such deal" when you next try to exchange a per-turn asset (gpt, resource) for a one-time asset (tech, cash).
BTW, without extensive testing, I get the sense that declaring with units in territory damages your rep, but declaring with units in territory and an RoP destroys your reputation.
A final thought -- it is quite easy to declare honorably, but accidentally break deals, causingg rep damage. This is particularly true in the Middle Ages. Trade routes are fragile and few, and a hasty declaration can cause a trade deal with a third party to be broken (causing a rep hit) simply because a "neutral" harbor, coastal water lane, or road falls under enemy control -- you suddenly have no trade route with a third-party trading partner.