Like others I'll just ad comments.
- There are TH addressable 5mm RGB LED's available. This may or may not be preferable to the SMT type.
- I'm sure I have seen large (120x450mm) stripboard prototype boards on ebay. You can solder the 6-pin 5050 or the 4-pin 5050 Addressable LED's directly to these, but will still require soldering an awful lot of jumpers on the back to hook the DOUT to DIN of the next one for either the 4-pin or 6-pin. For long runs you might want to use more than one strip for the power rail and ground, but the layout means its very easy to add decoupling caps distributed along the lines. If you insist on having a custom laysout for the LED's, this is probably the best combination of cheapness and convenience, whilst keeping functionality.
- As has been suggested, why not LED strips? They generally have decoupling caps on the strip, and the cheapest have low densities, ~30 LED's per metre which is ~1 5/16" spacing. Looks similar to what you have on those boards. They have self adhesive, easy-to-use connectors, and you can break them up into strips of only 8 LED's, and have 4 of those stuck to your MDF blocks. You would only have to wire connectors between strips (wiring three 4-wire connectors, rather than 4x8 =32). They are also dirt cheap, available everywhere, and have more options (RGBW, low profile - SK6812, waterproof etc..).
- 'Neopixel' is the brand for Adafruit Addressable LED's. You mentioned you get 50 for $5 which is a great price. Adafruit are often much more expensive. It seems like getting LED's on individual boards might be cheap, but as you found out is making life *more* difficult in terms of wiring.
Conclusion: Seriously, get some WS2812B strips. For ~ $20 you can get a few metres, which means you'll have lots spare should any LED's die - and replacing the strips will be easy if you use the snap-in connectors. It will greatly reduce the wiring time whilst still allowing the pattern you have in that pic, should be more reliable (less fannying about worrying about decoupling) and let you spend more time on other parts of the project. The cons? You're not doing something entire from scratch. but if that was the point of the project, then I'm sure you would be happy to do all that wiring.