Hi Jude, here are some possible answers to your questions:
LEDs: 1. they do not currently double as a 30 second display. They double (or actually their primary purpose is) as a way of monitoring the WWVB bits: zero (pink), one (yellow), mark (green), frame (blue) and error (red). They also makes a great way to watch a thunderstorm - the red flashes with every lightning strike within a hundred miles in the direction perpendicular to the antenna.
2. necessary? Not in order to function, but I wanted to play with some super bright LEDs I have, so I used them here - they range from 9000 mcd to 17000 mcd. As an alarm, they will wake me up! I used a transistor on each one, so I can run it at full current, without putting a large load on the Arduino pins (the LEDs draw 25ma each, but the Arduino only sees 5ma each.) Over kill I know. As a tribute to WWVB's cold war heritage, I used can type transistors from the early 1970s.
I have two alternate designs: one uses a single RGB LED, and the other uses one red and one green micro LEDs. I chose the big display for aesthetic reasons. I like a packed circuit board!
Output: 1. Right now I have it configured as a 24 hour clock - it runs from 0-23 and 0-59. However I'm still developing the display routines, so it's in flux. The mode switch (slide switch along the bottom, left of center) is used to change the display mode. I think I will incorporate what I call 'system time', where the values go 0 to 239, using almost the entire range of possible values. This works best for devices that do not need to be read by a human, as it gives much greater precision at the cost of readability. My ToD bit uses system time to control the position of the World Time globe.
2. I had not considered using an output for an alarm, but I don't see why that wouldn't work. My initial idea was to multiplex the alarm trigger as an analog value that is greater than the range of normal output. This is one reason system time only goes up to 240. The extra 15 can be used for control signals. But this part is further down on the list.
Button: I recently added the button. In one mode, it tells the device to immediately begin checking for the WWVB signal and set the clock. In the other mode, it does allow manual over ride, or alarm setting, using the HMS pots.
Input: Right now, input does nothing - the signal line goes to ground through a 1M resistor. I would like to use it, but haven't. Start trigger perhaps, for a timer?
Thanks for these useful questions Jude - they sure help guide my development of this module. I see that @blindbento has added more while I've been answering these, so I'll look at those next.