OK, sure you can program using the ISP header. But without making an attempt to bring out the Tx pin to a serial-to-usb converter you are working with your hands tied behind your back. Basically your debugging will be "does it work perfectly? or not?".
With serial prints you can check stuff (like your original question). You can see if code is entered and how often. You can see if it resets unexpectedly. You can see what numbers (where relevant) are coming into your analog port.
There are other debugging methods. I describe one here:
If you have the I2C pins free (or free for another device) you can send I2C debugging out to a second Arduino (or Atmega or whatever) and get your debugging via that.