Generally, bow thruster and windlass batteries are installed forward so the leads to the equipment are short with little line loss. The charging leads should only need to carry a lot less current and therefore do not need to be battery cable.
It sounds to me as though you just do not have enough amperage in whatever battery(s) you are using for the thruster and windlass by the time it reaches the equipment. You may need much bigger batteries as well as going up in voltage. You should be able to pull up your anchor without the engine or genset in an emergency.
On the other hand the thruster is a nice aid, but should never be considered a necessary tool for maneuvering a vessel. Therefore, I would plan my power consumption around this, making sure that you can get that pick up w/o the engine or genset. As most decent windlasses pull chain at around 60 feet a minute, it's pretty easy to figure out how long you must continuously operate the windlass to get up the scope you usually put out. Then determine the max consumption so this is no more than 20% of the total battery capacity. Then you should never have a discharge problem while using either piece of equipment.
The windlass manufacturers recommend taking the strain off the chain when pulling it up by powering forward. I find I often foul my chain around something on the bottom when we do this so we use the catenary effect of the chain to get the boat moving forward while we pick up.
As I'm sure you know, solar only gives you full output when the sun is unobstructed and mainly right overhead, so a 500 watt rating is only a small percentage of that over a complete day's sunlight. I wouldn't count on it as a reliable charging source, even in the tropics. I'm not certain about the new charge controllers, but generally speaking if you are going to double the voltage, you will halve the amperage, so I'm not sure there is an advantage in going to 24 volts there.