Yeah I made the mistake of going /nin to my first party. When you go /war, do you still use a 1-Handed Axe, or is it better to switch to a different weapon?
Axe is definitely best. Dagger and Sword aren't nearly high enough to be of use and Beastmaster doesn't get access to any of the decent Scythe weapon skills - some scythes will do better damage than axes at certain levels but since the weapon skill damage is so poor that it's generally just not worth it.
The large problem with BST/NIN is that BST will often come up short on both accuracy as well as attack, and no food can really effectively cover both. Because of this you're generally only able to go BST/NIN when you have access to a ME/Juggy combo (which allows you to use Sushi and still have relatively decent attack) or when you have access to dual Viking (which allows you to eat meat and still have decent accuracy).
The latter option can result in you doing great damage, however you may need things like PCC and snipers/woodsmen rings to be comfortable with the accuracy rate you'd wind up having vs some monsters. If you ditch a Viking for a Wrath Tabar at 56 then you might be forced to go back to BST/WAR due to the accuracy loss, however at 59 you can trade a Viking for a Kabrakan or Wrath and you should still be able to dual wield thanks to Hauby's acc bonus. You could also trade in a Viking for Wrath at 57, if you happen to have a SH you plan on using until 59.
Axes don't get much better from that point on until the 70s range, in which case you can get a Maneater/Juggernaut combo (Woodville/Maneater works almost as well) and pop Sushi without worrying too much about your attack rating. The issue until then, however, is whether or not you're comfortable with using a setup such as Wrath/Viking or Kabrakan/Viking til L70+.
Many people laugh at the concept of off-handing a Viking past L53 for some reason I'll never understand, since that accuracy boost can be enough to pop attack food which raises your DoT substantially as a BST...cutting straight to the point though, I'd recommend using Vikings (or offhanding a Viking when the time comes) if it allows you enough accuracy to pop attack food. If it's not enough, you should sub WAR and pop Sushi instead.
*Late edit* When you reach the later levels, there's an option some might notify you of: Gaudy Harness + Dual Rune Axes. With this and Sanction Refresh you get a +10 attack bonus and 10hp/tic auto-regen. This is fairly nice for solo, but is really -only- useful when solo. Or maybe if partied with a REALLY REALLY bad healer. =P
*More edit* Sorry if that was way too drawn-out. Pent-up nerdiness. <_<