Its annoying but you can get the weapon still. Just not the 100% guaranteed version. Besides, people treat it as the "end all, be all" item when really the game is easily manageable without it and is only "technically" the best game as both the Masemune and Tournesol are equally as useful and blatantly broken. Its a trophy item much like the Wyrmhero Blade.

I personally feel Excalibur 2 is more of a slap in the face than the Zodiac Spear. At least its possible to obtain ZS if you screw up with the treasure chests. Missing Score/HP Shout and Excalibur 2 are all one shot deals with no means of reacquiring without replaying an early save or hacking the game. The sheer demands for Excalibur 2 also simply suck the fun out playing IX. Its a trophy item and hardly worth the effort unless you just hate IX's story of which I would wonder why you would even bother trying to get the item.