Вот исправленный вариант.
Вы передавали один in на всех и попадали в гонку/deadlock.
#include <iostream>
#include <string>
#include <fstream>
#include <sstream>
#include <vector>
#include <deque>
#include <map>
#include <thread>
#include <mutex>
std::mutex mutex;
std::string files[4] =
        {
                "file1.txt",
                "file2.txt",
                "file3.txt",
                "file4.txt"
        };
void pipeline(std::string &in, std::vector<std::string> &str)
{
	std::lock_guard<std::mutex> lock(mutex);
	std::ifstream file;
	file.open(in);
    while (!file.eof())
    {
        std::string temp;
        std::getline(file, temp);
        str.push_back(temp);
    }
	std::cout << in << " finished" << std::endl;
	file.close();
}
int main()
{
    std::string string;
    std::vector<std::string> str;
    std::map<std::string, std::size_t> freq;
    std::deque<std::thread> pool;
    std::ofstream out("out.txt");
    for (std::size_t i = 0; i < 4; i++)
    {
        pool.push_back(std::thread(pipeline, std::ref(files[i]), std::ref(str)));
    }
    while (pool.size())
    {
        pool.front().join();
        pool.pop_front();
    }
	out << str.size();
	std::cout << str.size();
	std::cin.get();
    return 0;
}