The water alone was NOT what tripped the breaker. Water alone does not cause shorts and arcs. You have another issue somewhere in that cable run. Check every connection, box, splice, etc.
And yes, you could be doing more damage to the wire or breaker by repeatedly trying the breaker and tripping it so many times.
On another note, if you only have 12/3 going to a typical electric dryer (in the US I assume) that is NOT the correct cable. An electric dryer requires 10/3 on a 30A breaker.
Accessible or not
While you might call this area inaccessible because it's small, dark, and difficult to enter. In this case, the codes definition of accessible is whether or not there's permanent stairs or a ladder.
Cable run across the top of joists
If the attic is accessible by permanent stairs or ladder, any cable running across the top of joists will have to be protected. Protecting the cable is as simple as installing "substantial guard strips", which can simply be a 1x2 furring strip on each side of the cable.
If there's no permanent stairs or ladder, this protection only has to be provided to cables within 6 ft. of the entrance of the attic.
National Electrical Code
Chapter 3 Wiring Methods and Materials
Article 334 Nonmetallic-Sheathed Cable: Types NM, NMC, and NMS
334.23 In Accessible Attics. The installation of cable in accessible attics or roof spaces shall also comply with 320.23.
Article 320 Armored Cable: Type AC
320.23 In Accessible Attics. Type AC cables in accessible attics or roof spaces shall be installed as specified in 320.23(A) and (B).
(A) Where Run Across the Top of Floor Joists. Where run across the top of floor joists, or within 2.1 m (7 ft) of floor or floor joists across the face of rafters or studding, in attics and roof spaces that are accessible, the cable shall be protected by substantial guard strips that are at least as high as the cable. Where this space is not accessible by permanent stairs or ladders, protection shall only be required within 1.8 m (6 ft) of the nearest edge of the scuttle hole or attic entrance.
(B) Cable Installed Parallel to Framing Members. Where the cable is installed parallel to the sides of rafters, studs, or floor joists, neither guard strips nor running boards shall be required, and the installation shall also comply with 300.4(D).
Cable run through bored holes
You could always run the cable(s) through holes bored in sanw lumber joists, but you'll have to make sure the edge of the hole is more than 1 1/4" from the nearest edge (2" according to IRC).
National Electrical Code 2014
Chapter 3 Wiring Methods and Materials
Article 300 Wiring Methods
300.4 Protection Against Physical Damage.
(A) Cables and Raceways Through Wood Members.
(1) Bored Holes. In both exposed and concealed locations,
where a cable- or raceway-type wiring method is installed through bored holes in joists, rafters, or wood members,
holes shall be bored so that the edge of the hole is not less
than 32 mm (1 1/4 in.) from the nearest edge of the wood
member. Where this distance cannot be maintained, the
cable or raceway shall be protected from penetration by
screws or nails by a steel plate(s) or bushing(s), at least
1.6 mm (1/16 in.) thick, and of appropriate length and width
installed to cover the area of the wiring.
NOTE: When dealing with engineered structural members, boring holes may not be an option.
Best Answer
It's acceptable to leave wire in the walls. The only thing you need to do is leave the ends exposed in boxes and wire nut and tape the to legs together. That will indicate to an electrician what's going on, and if someone does try to tie into them in the future it will just pop the breaker.