I was able to make it work thanks to the advices of Lundin and JimmyB in the comments.

NOTE: This code works on my phisical Esp32(DEVKIT 1) since I got it. I have not tested it on the emulator.

What I was missing:

• enabling the clock in register DPORT_PERIP_CLK_EN_REG
• resetting timer after it has been configured

What I discovered:

• to make the channel use the new duty value it has to be (re)started (bit 31 in LEDC_HSCH0_CONF1_REG)

I post here a working code in case someone gets stuck like me.

#include <stdio.h>
#include <unistd.h>
#include <inttypes.h>

#define GPIO_OUT_W1TS_REG (*(volatile uint32_t*)0x3FF44008)
#define GPIO_OUT_W1TC_REG (*(volatile uint32_t*)0x3FF4400C)
#define GPIO_ENABLE_W1TS_REG (*(volatile uint32_t*)0x3FF44024)
#define GPIO_ENABLE_W1TC_REG (*(volatile uint32_t*)0x3FF44028)
#define GPIO_FUNC0_OUT_SEL_CFG_REG 0x3FF44530
#define LEDC_CONF_REG (*(volatile uint32_t*)0x3FF59190)
#define LEDC_HSCH0_CONF0_REG (*(volatile uint32_t*)0x3FF59000)
#define LEDC_HSCH0_CONF1_REG (*(volatile uint32_t*)0x3FF5900C)
#define LEDC_HSCH0_DUTY_REG (*(volatile uint32_t*)0x3FF59008)
#define LEDC_HSCH0_DUTY_R_REG (*(volatile uint32_t*)0x3FF59010) 
#define LEDC_HSCH0_HPOINT_REG (*(volatile uint32_t*)0x3FF59004)
#define LEDC_HSTIMER0_CONF_REG (*(volatile uint32_t*)0x3FF59140)
#define IO_MUX_GPIO26_REG (*(volatile uint32_t*)0x3FF49028)
#define DPORT_PERIP_CLK_EN_REG (*(volatile uint32_t*)0x3FF000C0)
#define DPORT_PERIP_RST_EN_REG (*(volatile uint32_t*)0x3FF000C4)
#define LEDC_HSTIMER0_VALUE_REG (*(volatile uint32_t*)0x3FF59144)
#define resolution (uint)8

void app_main(void)
{
    printf("test\n");

    DPORT_PERIP_CLK_EN_REG |= (1<<11);// enable clock for ledc

    LEDC_HSTIMER0_CONF_REG &= ~(0xf);
    LEDC_HSTIMER0_CONF_REG |= resolution; //resolution = 8 bit
    uint divider = 80000000 / (5000 * 256);
    LEDC_HSTIMER0_CONF_REG |= (divider<<13);


    LEDC_HSCH0_CONF0_REG &= ~(0b00); //timer 0
    LEDC_HSCH0_CONF0_REG |= (1<<2); //enale output channel

    LEDC_HSCH0_HPOINT_REG = 1; // value to set high
    LEDC_HSCH0_DUTY_REG &= ~(0xffffff);
    LEDC_HSCH0_DUTY_REG |= (20<<4); // low duty cycle
    uint low = 1; // flag to control next duty value

    // gpio setting
    volatile uint32_t* gpio26_cfg = (volatile uint32_t*)GPIO_FUNC0_OUT_SEL_CFG_REG + 26;
    // peripheral 71 -> hschan0
    *gpio26_cfg = 71;
    GPIO_ENABLE_W1TS_REG |= (1<<26);
    // function 2
    IO_MUX_GPIO26_REG &= ~(0b111 << 12);
    IO_MUX_GPIO26_REG |= (2<<12);

    LEDC_HSCH0_CONF1_REG |= (1<<31); // start channel duty cycle
    LEDC_HSTIMER0_CONF_REG &= ~(1<<24); //reset timer
    uint counter = 0;
    while (1) {
        if (counter == 2){
            if (low == 0) {
                LEDC_HSCH0_DUTY_REG &= ~(0xffffff);
                LEDC_HSCH0_DUTY_REG |= (30<<4);
                low = 1;
                LEDC_HSCH0_CONF1_REG |= (1<<31); // start channel duty cycle
            } else {
                LEDC_HSCH0_DUTY_REG &= ~(0xffffff);
                LEDC_HSCH0_DUTY_REG |= (128<<4);
                low = 0;
                LEDC_HSCH0_CONF1_REG |= (1<<31); // start channel duty cycle
            }
            counter = 0;
        }
        printf("timer value: %" PRIu32 "\n", LEDC_HSTIMER0_VALUE_REG);
        printf("duty value: %" PRIu32 "\n", LEDC_HSCH0_DUTY_R_REG);
        printf("counter: %d\n", counter);
        sleep(1);
        counter++;
    }
}

Since I am a newbie in C please feel free to correct me as Lundin did, I will appreciate it.