This question is continually asked - particularly regarding USN nuclear subs - and answered, which - again, for (at least) USN nuclear subs - appears to be: WHATEVER THE CAPTAIN WANTED (subject, of course, to his logistical constraints, at the time).
Thus, sometimes hull-bottoms were painted Hull Red, starting exactly halfway down (at the maximum beam of) the hull - other times, starting at the nominal (Plimsol) waterline - and yet other times, hull-black or -gray, simply extended down from above. Many historical pics (of subs obviously not having drydock availability) show a topside black, or gray, painted right down to the actual waterline - i.e., usually lower forward than aft, as subs usually go about (even when tied up at the wharf) trimmed-down by the stern, at least to some degree.
However, notwithstanding the above, the nominal paint colors on The Real Thing are almost never exactly what a model must be painted, in order to look (or invoke a "feel") at all realistic:
Here is what the Real Deal looks like: the Ohio-class boomer Pennsylvania, on parade July 20, 2005. Nominally she would be described as painted Black to the (nominal) waterline, with Hull Red below - plus a medium- and a light gray, appearing respectively on the bow dome and various small, circular covers on the deck: (3) pairs of Ballast Tank vent-covers, and what appear to be various small sensor windows, flush on the hull. Four "colors" - that's it.
However, painting a model in just four colors, selected to match the above descriptions, would leave it woefully inadequate in its portrayal, which would miss at least six additional finishes, visible above. Note, for starters, just the basic "Black" alone exhibits three additional finishes: 1) glossy and much darker when wetted; 2) darker-still, when submerged; and 3) matte-finish (which can look darker or lighter, depending on the viewing/lighting angle), over non-skid-treated areas. Yet a fifth "black", lightest of all (at least, when viewed from this angle), appears to be on the (retracted) mast-tops - which I labelled "older/faded" - but these could as easily be a bona-fide different, lighter-gray (camouflage) paint, and/or radar-absorptive coating.
Even if the masts above are a special case, still there are numerous patches on the deck where either the paint and/or non-skid coating is newer, and therefore a different (presumably darker) shade. Likewise, note the mottling on the sail planes - which I put down to burnishing (basically polishing) by rubber-soled deck shoes - or, it could as easily be complete wear-through, reavealing underlying patches of older paint. Or just the opposite: numerous spots of (darker) touchup paint, on unprotected, yet relatively high-traffic surfaces.
Note convincing depiction of the above "blacks" could only use one, true "black" color right out of the bottle: Gloss Black, for the darkest (i.e., the submerged) areas. All the rest would have to be combinations of lighter-, semi-gloss and/or matte-finish grays - varying from the very dark all the way through medium-light. Similarly, note the very light gray, nearly off-white, ballast tank vent-covers are noticeably brighter - likely less glossy, as well - when completely dry, as opposed to wetted, which can be seen is the case for the forward-most pair (upper left).
And finally, note the Hull Red - everywhere wetted - emits only the slightest reddish hue, losing even this all but completely on submergence by just the first few inches (bottom-right), leaving a near-neutral gray.
Of course, modelled water - using acrylic gel, or similar - will automatically create some of the above effects - however I would argue not sufficient to overcome the "scale effect" (which is usually primarily about diffuse indoor lighting, especially of smaller objects).
Meanwhile, most full-hull builds do not even seek to invoke the "look and feel" of any submerged area(s) - despite the fact they often depict fouling on precisely these areas (and of course, weathering overall). To each his own, of course. But personally, I don't "get" this, and in fact would consider depicting submerged/wetting effects before weathering (if at all).
In any case the truest, complete answer to the question, "What color was my sub?", will in fact always turn out to be something along the above lines.
HTH - Cheers,