Do your Toyota breathers breath in both directions or are they like my Tacoma ones that have a check valve? In the original location the check valve was critical to keep water out for short water crossings, but if you sit in water long enough they can let water in anyway. After you extend the line to the check valve breathers and leave the check valve on it, it can let air out when getting hot, but when you go through water it doesn't let air back in, so water can get sucked in through the axle seals.
I use fuel filters on the end for the FJ40 extended breathers, and took the rubber flapper out of the check valves on two of the Taco ones and put fuel filters on the other two after I extended them.
The check vale in the breather isn't a real tight shut-off, so it eventually allows air back in. I don't have personal experience with water getting sucked through axle seals before I extended and modified them, but that's the InterWeb's theory.