Here are my thoughts:
1. How many digits do you need for the counter? Each digit requires 7 digital outputs (one for each segment) unless you get a clock module that communicates in some other way (like a binary input, or some sort of digital communication), and the SBC only has 8 digital outputs. Also, the larger 7-segment LEDs usually require 12V, so the digital outputs on the SBC wouldn't be powerful enough to turn on the LEDs. You'd need relays or transistors in combination with the SBC's outputs to switch up to 8 such LEDs. The open-collector digital outputs on the 1012 would be capable of this task. Here's an example of a big 7-segment LED
2. Depending on how simple the sound can be, you can go simpler than a small speaker. A piezoelectric buzzer is a cheap way to make noise and all you need to do is apply voltage to it (5 or 12V depending on the buzzer- if 12V, then you'd need a relay or transistor to switch power to it). You may also be able to find digitally-triggered alarm modules that already contain a speaker and all of the necessary circuitry. If you must use a speaker, you'll need to get a USB-to-audio adapter for the SBC and install drivers and software libraries that enable its use.
3. Of the languages you know, I would recommend Python because Matlab and VB are a bit more limited in what they can do and it's harder to find programming help online. If you're looking for a new language to learn, C# has a wide user base so it'll be easy to find help when you're stuck. Either way, the code for this program should be straightforward enough.