Depends on DM ruling.
If destroying the surface the Explosive Runes are on successfully destroys the Explosive Rune without setting it off, then potentially only one of those 2,000 Explosive Runes you set up actually hurt anyone (no loopholes to this strategy of keeping that particular abuse out, unless you give the party something that can ignore force damage pretty much completely).
Do note that the same spell overlaps, it doesn't stack, and the Explosive Runes spell targets an object, and causes particular properties on that object - the explosion; if you put two on one book, you still only get one set of damage dice (loophole: player enchants individual parchments, tied together with string, rather than spellbooks; area dispel, all unattended objects in the area are potentially effected - so you can still get 1,000 of them going off).
Make the player roll and total up those 12,000 d6's, just to see how long the other players will stand it (Loophole: after finding out about this the hard way, a player will just set up as many as he can stand - which will still probably reduce any BBEG to a smoking crater - rather than as many as he can pack in).