The boards are relatively cheap, have an on-board debugger. Arduino has improved over the years, perhaps more libraries and a relatively low complexity to be had there. The real power is programming the MCU natively, using interrupts, RTOS, etc. On the NUCLEO you have the benefit of the Arduino shield format, but also the breakout of most MCU pins to headers.
People use them to prototype all sorts of complicated designs. If you want screens and more integrated features, but less available pins, try looking at the DISCO and EVAL series boards. The EVAL boards being designed to allow testing of most all features of the MCU, and there is BSP (Board Support) and HAL examples built around them. For custom boards these can be ported based on pin/part choices.
STM32Cube MX/IDE is an automatic code generator and IDE for those that like that level of complexity. Saves reading Data Sheet and Reference Manuals until there is a problem. The HAL is a library that provides a common view of the hardware across numerous STM32 models.
You can connect an oscilloscope or logic analyzer to any pins you want, and have access too. Most pins are exposed on the Nucleo boards
