Stand Your Ground And Fight
When you think of combat in RPGs it tends to break down into two types of fight: L5R fights, and Shadowrun fights.
L5R fights start with everyone knowing who is there - and sometimes who is who and a pre-fight cup of tea - then you roll initiative and get into the combat. This happens a lot in L5R (hence why I call it that) because Rokugan is a setting where honor is very much steeped into everything, even the bandits sometimes. Sure, ambushes do happen, but in the L5R games I've been in they've been rare. Most times you know you're getting into a fight and are on the combat timer before an attack is rolled.
Shadowrun fights are the exact opposite. In Shadowrun there is no honor - at least not the type the Akodo in L5R are looking for - and it is very much about being efficient and surviving. When a sizable portion of your paycheck could be going into new ammo - or replacing lost and damaged gear - you take pains to fix that. Because of this, most Shadowrun PCs don't fight fair. If they can't ambush, they don't engage. If they can ambush, they kill everyone before the surprise round is over. It's just safer.
So what indeed. Between the two types of fights we end up with three key scenarios.
- The NPCs ambush the PCs
- The PCs ambush the NPCs
- Neither side ambushes the other
You want to consider heavily which one is likely to happen when designing an encounter, because this is a difficulty multiplier. Flat out, if the bad guys get a free round of attacks before the PCs know what is going on, the encounter is going to be a lot harder - and some PCs may never get a chance to participate in the fight. The same is also true in reverse. If the PCs get to ambush the NPCs, expect that you won't be getting to use the abilities on at least some of those NPCs.
The third type is just a straight fight.
Sending A Message vs. Being A Bad Ass
There are two other big reasons to use the ambush method, or give opportunities for it. NPCs that ambush are going to send a message to the PCs - and that message is to be alert for ambushes. They may hate the NPCs/creatures that do this. They may take a more "shoot first" approach. The point is, when you use tactics like ambushes, your PCs will respond in kind.
Sending a message though can also be done to show how something has changed. If the PCs have fought dozens of goblins that were more or less straight up fights, suddenly having goblins that use their ability to hide mid combat to maneuver and ambush can send a message that this goblin leader is a more sinister foe.
On the other hand, by giving the PCs a chance to ambush or prepare the battlefield, you can give them chances in fights that they otherwise would have no chance in. Sure, 5 creatures of a CR equal to the party is going to be overkill by the rules, but let the PCs ambush and isolate those creatures and it's barely a problem. Plus, the PCs feel badass and it promotes team work inside the group. Getting the PCs to work as a team is awesome and opens up a lot of possibilities in the game.
Other Things For Tweaking
Beyond "being ambushed makes it harder" and "ambushing makes it easier" there are other things you can tweak in encounters to make them harder or weaker.
Consider the PCs coming across a dragon. If they're low level that's beyond them, but what if they come across a dragon that's limping home from destroying a town? Now it's hurt, down on HP, out of spells, and with its breath weapon potentially exhausted. Can they take it now? What if the dragon will flee at a certain HP level?
My point is this: play with your scenarios. Give the PCs chances to ambush and use tactics. Hit them with those same tactics. Have them show up late to a fight to find the victor still has some strength in him. Have them fight things that will flee to save their own lives.
Make it real, but keep an eye on the difficulty bar while you do so. Everything you tweak is going to make it harder or easier depending on what you're doing and how the PCs handle it.