Can Cura alert me (give a warning) if it estimates times for layers are too long?
Look at Cura's cooling settings. It doesn't have a warning like you asked for, but it does have options to control the fan to avoid over-cooling. I think you need to set "Regular/Maximum Fan Speed Threshold" to the number of seconds you want to consider a "long time" for a layer to take, then set "Regular Fan Speed" (for layers that take a long time) to 0 or something low, and "Maximum Fan Speed" to 100 or whatever you normally want to be using.