laws in the way they affect people
could be written as:
laws in the way in which they affect people
For this second fragment, is the meaning of the first "in" the same as the second "in"?
Short answer: They are the same.
We can understand them as, according to Macmillan Dictionary,
Adjective, Adverb, Preposition
10. used for talking about the way something is done
a. using a particular method or style
We are trying to teach mathematics in a more interesting way.
The houses are all built in the traditional style.
You have to pay in cash.
b. used for describing a particular type of behavior or way of speaking
We all sat in silence.
She called out to me in a loud voice.
Actually, we can understand the two ins in your phrase without having to rely on any special entry in dictionaries (such as those that include in the way or in which).
For example, let's consider this dialogue:
A: Let's take a look at these laws.
B : Why are they important?
A: Because they affect people.
B: How do they affect people?
A: They affect people in the way they affect people, of course. (This is blunt and it's circular (tautology), but we can't say that what A said is incorrect.)
B: How would you like us to consider them?
A: I think we should consider them in this way--the way they affect people.
B: Aha. I see. They are laws that affect people in some specific way. And you want us to consider them in that way. In other words, we are going to consider these laws in a specific way. And, these laws affect people in that specific way.
A: Could you rephrase it?
B: Sure. We have these laws, in this specific way, in which they affect people.
(C walks into the room)
C: What do we have to work on today?
A: These laws in the way in which they affect people.
Let's take a closer look at what B said.
We consider these laws in a specific way.
These laws affect people in that specific way.
Let's replace some words to make it more resemble your phrase. Then we pied-pipe it and merge the two sentences in the process. (See more details about pied-piping in this answer.)
We consider these laws in a specific way. These laws affect people in that specific way. ↓ ↓ ↓ We consider these laws in [the] way. [They] affect people [in which]. ↓ ←←←←←←←←←←←←←←←←←←←←←←←←←←← ↓ We consider these laws in [the] way [in which] [they] affect people.
And now, we have your phrase:
We consider these laws in the way in which they affect people.