So, in one of my most recent Order vs. Order games, my opponent trained 5 ninjas and started attacking my army (even as I tried to make my army run here and there to avoid Shinobi) and he pretty much succeeded in obliterating half of it. Then they started picking off my walls, and my army of 3 (fire-arrow enabled) flying crossbowmen, 5 archers, and a castle archer did nothing to stop that.

Several questions regarding strategy:

1. How do I outmaneuver ninjas to avoid getting hit by Shinobi?

2. How do I effectively defend in the above position?

And, if you can answer this next one:

3. Later in the game, I finally trained a maxed giant but I was forced to quit due to my environment (let's just say I was playing under cover) (unfortunately my recording was lost as I'm a non-member)

At the time of my resignation, the armies were as follows:

Me: 2 castle archers, maxed giant, 3 albowtross (fire bolts enabled), 3 archidons (fire arrows enabled), 2 walls (just a little in front of my first cluster of gold mines), 4-6 miners
Opponent: Lowest-health giant, 7 archers (fire arrows enabled), 4 ninjas, 3 albows (fire bolts enabled), maybe a couple speartons

How would I properly defend this position?

The moment I see an ninja I just spam albows/wings and occasionally throw in support units but I don't rely on them because ninjas are quite good at killing them fast. What a decoy Meric/Spear does do however, is make the ninjas go directly under my albows and take loads of damage as they retreat. I rarely kill a ninja outright in one encounter but if you keep pressuring them then they don't get a chance to heal back up.

Most reasonably fast units can outrun ninjas in shinobi mode, so use that to your advantage too.

A good way to deal with it can be to mass archers, speartons and 2 or so merics. After that, set up a miner wall and shield wall the speartons ON TOP OF THE WALL. That way the ninjas will almost always attack your speartons instead of the wall, resulting in them getting shield bashed and killed. If your wall does go down and some ninjas get through to kill your merics, wait a moment. If the ninjas run, keep your speartons as they are to stun them as they run. If they continue attacking your troops, unwall your speartons and slaughter them.

Quote from TheMasterFez

A good way to deal with it can be to mass archers, speartons and 2 or so merics. After that, set up a miner wall and shield wall the speartons ON TOP OF THE WALL. That way the ninjas will almost always attack your speartons instead of the wall, resulting in them getting shield bashed and killed. If your wall does go down and some ninjas get through to kill your merics, wait a moment. If the ninjas run, keep your speartons as they are to stun them as they run. If they continue attacking your troops, unwall your speartons and slaughter them.

For that to work well you have to have a decent mass of archers already up when you see the first ninja, otherwise the ninjas will play guerilla tactics and keep picking off your archers without casualties themselves.

Albow massing is a lot safer

One way to stop ninja massing is to stop it before it begins. One way to know it is if the opponent is playing defensive with a castle archer. If that's the case,build a wall as far out as you can,get a spearton to tank and some archers to harass. If you fail to defeat him early however, it's best to just do what skeletonxf said.