Most commonly, a fuse is used to protect wiring. If the controller has a fault that causes the fuse to pop, it most likely has a big problem and is toast anyways. No fuse would simply allow the fault to correct itself, typically by going up in smoke. Lets say you are using the fuse to 'protect the controller'. This would most likely mean you want to protect the controller from an overcurrent situation, since thats about all a fuse could possibly do. You would size the fuse for something around or a bit over the peak current you run. Now, lets imagine for whatever reason the controller starts drawing way more current than usual for long enough to pop the fuse. The controller is likely already drawing more current than it can reasonably tolerate, and all of a sudden the fuse pops. Now the battery is no longer connected to ballast any inductive kick. Since there likely exists some considerable enough inductance from where the fuse pops up until the controller, you will see a large inductive voltage spike on the controller, quite likely damaging it anyways. If the components are running way under the max spec, they might be fine. However, if the controller is running near its limits, it's probably going to have an issue.
For low voltage systems most standard fuses will work fine. Typically, they can actually be effective on low current systems. However, once you start talking about high voltage and high current systems, common fuses often offer very little, if any, real protection for components. Plus, most batteries with a BMS don't really need a fuse at all. I wouldn't bother running a fuse on a SLA battery unless it's a BIG pack, but thats just me. At 24 or 36V the average fuse with a reasonable current rating can provide some limited protection. It will most likely help most if you like to connect things backwards. Past that they don't help much for ebikes.