First off, glad you like the game. Read up on the strategy guides (if you haven't already) and look into the mechanics of the abilities. There are a lot of abilities that go well together. Also, don't forget all the acronyms we throw around. Trust me, there are a lot...
1. No, it just goes straight through the cap unfortunately. The exception to this is Cleansing Brilliance/CB which can go through ships, but it doesn't ignore them, it damages them just as much as the target.
2. You can hide outside of a ship's firing arc. This is hard to do though when facing Illuminators as their side beams (very deadly ones at that) can still hit you a good chunk of the time.
For nitty gritty, this is called Microing. If you like microing, I'd suggest playing as Advent or Vasari as they require the most. Advent ships have synergies, or groups of abilities that work well together. Example:
Holy Trinity: this is a general name for the three primary Advent capitals-Progenitor Mothership, Halcyon Carrier, and Radiance Battleship. Each one is wonderful alone but combined, they are the best cap-ship combo in the game.
Cleansing Brilliance/CB+Malice: When used by an expert, this allows you to deal up to 1000 damage per second/DPS to an enemy which will destroy any cap your enemy might have.
Animosity+Vengeance: Animosity makes them fire at one of the hardest ships in the game to kill which then reflects damage back to the attackers thanks to Vengeance
Amplify Energy Aura/AEA+Radiance Battleship: AEA is a great passive which increases DPS by 23%. On the Radiance, this is a very good buff.
For the TEC, there is the Dunov+Kol synergy. Flux Field+Gauss Rail Gun/GRG is awesome as it allows you to spam GRG and deal about 200 DPS for quite some time. If you throw in friendly culture and Finest Hour, you can fire for a minute straight.
I suppose the biggest tips would be:
1. Expect human players to Focus Fire/FF your capitals
2. Don't spam the Novalith. It annoys people but doesn't do that much. A Deliverance Engine/DE spam will cause big problems for the enemy though.
3. Don't underestimate the power of Repair Bays, especially if playing as the TEC. These things will save your fleet when on the defensive.
4. A fleet is better than any static defense outside of starbases/SB's.
5. Don't use Light Frigates/LF's after the first 10 minutes of the game. Switch to...
6. Long Range Frigates/LRF's are one of the most common ship spams because they are good. Illuminators dominate this category with their side beams.
7. Beware the Advent's Iconus Guardian. Repulse is a fearsome tool in the right hands.
8. Beware the power of the Advent. This race is pure military and can take two-three and sometimes four times as many TEC ships and win.
9. Beware the power of the Holy Trinity. Each one is powerful, but the combination of those three ships escorted by Illuminators, Dominas, and Guardians is a fearsome fleet.
10. Beware the might of Missile Barrage. When you see a level VI Marza in the gravity well, expect to take heavy losses. Missile Barrage/MB is the most powerful multi-target ability in the game (CB is the best single-target). It deals 3000 damage to all enemy ships within range over 25 seconds. If someone uses this on you, move your fleet or use Ion Bolt/Phase Out Hull/Detonate Antimatter/Reverie to stop it. The Marza can't move or fire normal weapons while using this ability so take the opportunity to leave. If you have a tight fleet formation and a Progenitor, you can actually sit there and just absorb the damage, although this is not recommended. Deactivate MB so you don't have to waste Shield Restore's healing power on making up MB's damage.
Well, there are some general tips... You didn't exactly ask for them, but oh well...