I wouldn't go drilling a lot of holes - even using a No. 80 bit is going to be too large for things like 1/700 masts and yardarms. Itt bitty dots of gel-type superglue where you want the rigging to go will be more than sufficient.
I tend to use stretched sprue colored with a black or brown permanent ink marker for a couple of reasons: 1) It's free, so I can afford to screw up frequently and make it any diameter I want, and screw up frequently, and 2) It is usually fairly rigid, even for long runs between attachment points. If it sags or bows a little after all is said and done, it can be tightened up with a match. Light the match, blow it out, and then wave the smoking head under the line in question.
And if this is your first ship in 1/700 scale, I wouldn't get too hung up about the rigging, especially on a warship. A line on the correct mast or staff for the national ensign, maybe a few on the signal yards, will be more than enough to make the ship look "busy."