Assuming 120 str and a +9 thanatos katar, the %atk boosts will probably be better than the FS enchants (assuming we're comparing say... atk 3% to FS 3; things change if you're comparing atk 1% to FS 8).
At +9, the thanatos katar already gives you 318 attack which your STR (at 120) will boost by another 60% of the base weapon attack (so 220 x 0.60 = 132), giving you over 450 weapon attack (this is not counting any extra STR from job bonus/vipbuff/blessing/etc. or even any equip attack from backpack or gangster scarf or whatever.
At this point, 1% of 450 = 4.5 atk... so 3% = 13.5 atk which means that 3% is better than FS 3 which gives 12 attack.
This will continue to be larger and larger the more attack you can stack, of course. So if Eddga procs, or if you have a wakwak card, or your temporal STR boots give you another 71 atk... all that will go through the % modifier too.
EDIT: The general rule is that if you already have 400 attack from weapon+equip, then % is better than FS of equal levels (atk 3% > FS 3). If you have less than 400, then the flat attack of FS is better.
As for the EDP portion, EDP favors weapon attack more than equip attack. Since the % mods can increase weapon attack, but the FS additions can't... that means EDP favors % mods as well.
Edited by mildcontempt, 30 September 2015 - 11:46 PM.