The physical part of the attack does but the lightning hits regardless.
Not really. Most of the lightning attacks operate differently from each other (exception- Charged Strike and Lightning Strike).
- Power Strike = Physical portion *AND* Lightning portion both depend on an AR check.
- Charged Strike, Lightning Strike = Physical portion depends on an AR check, the lightning portion (Charged Bolts or Chain Lightning) is autohit.
- Lightning Bolt = Lightning portion is autohit. Since it converts all physical damage to lightning damage, there is no physical portion.
- Lightning Fury = Both physical and Lightning portion are autohit
As you can see, even if your AR was 17 and you were level 12, Lightning Fury would land its physical damage 100% of the time. This makes LFury a great tool for leeching when you have brutal AR, because it always hits, always deals physical damage, and always leeches. This also means that Lightning Fury is a decent way to take down Lightning Immunes, since its physical damage is exactly like the physical damage from a standard throw, but it costs some mana and is autohit.
Anyway, as for whether Bowazons or Javazons are better... personally, I think Javazons are much easier for PvM. They're more powerful, and they can be built with much, much cheaper gear (you could honestly kill in Hell with no weapon except for a Cracked Javelin). They're perhaps the best group killers in the game (thanks to Lightning Fury)... and they're also perhaps the best single-target killers in the game (thanks to Charged Strike).
With that said, Bowazons are very fun, and Guided Arrow is the 'zon's best PvP skill. Make whichever 'Zon-type you think would be a bigger blast to play. Or you could always make a Hybrid, too. There's Lightning Javazons with 20 points in Strafe, there's Freezing Arrow Zons with 20 points in Lightning Fury, and there's Multi/Strafe-zons with 20 points in Lightning Fury (the 3 most popular hybrids).
Even if you make a Lightning Fury Amazon, my favorite trick is to keep a 6os Long Battle Bow stuffed with 6 Perfect Sapphires on switch, and to put one point in Freezing Arrow. Firing of a Freezing Arrow with a 6PSaph bow will freeze targets for a whopping 5 seconds in Hell (20 seconds in Normal, and 10 in Nightmare), without requiring a single other piece of gear. Very handy against tough monsters who are immune to your primary attacks, so you can pin them in place and let the Merc take them out.
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