This is a known downside with water bladders. In my opinion it's the largest downside of a water bladder compared to a water bottle. You don't know you're running low on water until you're completely out, and even then it's hard to tell if you're actually out of water or if you just got a kink in the hose.
The main benefit of a water bladder is that the easy, hands-free drinking makes it easier to stay well hydrated. If uncertainty over how much water you have left is stopping you from staying well hydrated, you're missing out on the main benefit of using a water bladder.
The solution is having more than one water container. That way when you run out of water in your water bladder, you have more water. There are two basic ways to do this:
Carry a full water bladder as your main water supply, and have a small "backup" or "reserve" of water in a bottle. Drink freely from your bladder without fear of running completely out of water, because you know there's always a little bit left after you do. If you do run out of water from the bladder and you're not almost done with your hike, that's the time to start drinking conservatively. But you don't need to conserve too much, because having to stop and drink from a water bottle will naturally reduce how much you drink.
Carry two water bladders, with half your supply in each bladder. Both bladders can go in the same water bladder pouch. You can run one drinking tube out of either side of your pack to start with, or you can keep the top of one tube inside your pack and swap them when the first bladder runs dry. If you're trying to keep pack weight minimal and don't mind a bit of inconvenient fiddling around, use one drinking tube and switch it between bladders. When you run out of water in the first one, you know you're halfway through your supply. If you're not at least halfway through your hike at that point, drink a bit less frequently. If you get to the halfway point in your hike without finishing your first water bladder, you can drink more frequently than you have been.
A few useful tips that came up in the comments section:
A water bottle can be more convenient to drink from during rest breaks, when you're not wearing your pack.
If you drink your bottle dry during a break, you can refill it from the hose of the water bladder. It helps if the pack is higher than the bottle (eg, if you're wearing the pack, hold the bottle down near your waist).
You can get an inexpensive, lightweight bottle in just about any size by reusing a drink bottle. For a 1L of 750mL size, I like sport drink bottles (eg, Gatorade or Powerade) or Smart Water bottles. Sport drink bottles are relatively sturdy because the bottles have ridges for reinforcement. Smart Water bottles are an unusual shape, tall and skinny, which may be useful for fitting them into a small water bottle pouch; I also find the drinking tops very easy to drink from, but the flip tops do tend to break after a while. Single-serve soda bottles are not as durable, but they're widely available and easily replaced when they get damaged. For a mini bottle (~250mL), look for children's drinks or juice, or small soda bottles.