Using uxQueueMessagesWaiting to get a semaphore's count works as expected for me. Here is a demo excerpt:

// uxQueueMessagesWaiting Demo
int dummy_value = 3;
xQueueHandle demo_queue = xQueueCreate(5, sizeof(int));

// Initial size is 0
if (demo_queue != NULL)
{
	unsigned int q_size = uxQueueMessagesWaiting(demo_queue);
	// Output q_size here; should be 0
}

// Push 3 items
portBASE_TYPE xStatus;
xStatus = xQueueSendToBack(demo_queue, &dummy_value, 0);
xStatus = xQueueSendToBack(demo_queue, &dummy_value, 0);
xStatus = xQueueSendToBack(demo_queue, &dummy_value, 0);

// New size is 3
if (xStatus == pdPASS)
{
	unsigned int q_size = uxQueueMessagesWaiting(demo_queue);
	// Output q_size here; should be 3
}

Which yields the expected output of 0 and 3.

From my tests, the number of tasks pending on a semaphore does not seem to impact the count.

Note: Using uxQueueMessagesWaiting with semaphores seems to be undocumented, unless I missed something.

Edit: I realized that my sample didn't actually use a Semaphore. The following sample verifies uxQueueMessagesWaiting for semaphores with both zero and non-zero init_count.

// semaphore queue size demo
SemaphoreHandle_t semaphore_handle1 = xSemaphoreCreateCounting(20, 0);
if (semaphore_handle1 != NULL)
{
    unsigned int q_size = uxQueueMessagesWaiting(semaphore_handle1);
    // Output q_size here; should be 3

    xSemaphoreGive(semaphore_handle1);
    xSemaphoreGive(semaphore_handle1);
    xSemaphoreGive(semaphore_handle1);

    q_size = uxQueueMessagesWaiting(semaphore_handle1);
    // Output q_size here; should be 0
}

// semaphore queue size demo (with init_count > 0)
SemaphoreHandle_t semaphore_handle2 = xSemaphoreCreateCounting(20, 5);
if (semaphore_handle2 != NULL)
{
    unsigned int q_size = uxQueueMessagesWaiting(semaphore_handle2);
    // Output q_size here; should be 5

    // Give 3
    xSemaphoreGive(semaphore_handle2);
    xSemaphoreGive(semaphore_handle2);
    xSemaphoreGive(semaphore_handle2);

    q_size = uxQueueMessagesWaiting(semaphore_handle2);
    // Output q_size here; should be 3

    // Take 4
    xSemaphoreTake(semaphore_handle2, portMAX_DELAY);
    xSemaphoreTake(semaphore_handle2, portMAX_DELAY);
    xSemaphoreTake(semaphore_handle2, portMAX_DELAY);
    xSemaphoreTake(semaphore_handle2, portMAX_DELAY);

    q_size = uxQueueMessagesWaiting(semaphore_handle2);
    // Output q_size here; should be 4
}

Output:

Semaphore Size (init_count == 0):0
After giving 3 times:3
Semaphore Size (init_count == 5):5
After giving 3 times:8
After taking 4 times:4