The idea was made for two big reasons.
1st: The intent of the ship was that it could operate alone and in deep space. As a result, it could run into many groups that might interpret the symbols/crest as a different nation. To avoid that, it was simply colored in NSN colors with gold-colored turrets to highlight it.
2nd: The ship can be painted black and given the crest if it's expected to serve in a more traditional/war capacity. Essentially, the profile and shape of the ship means that placement of the symbols has little value but can be done if the Jackdaw is expected to fight in close-quarters where even a small symbol on its sides can be identified.
If need be, lemme know and I guess I can remove that bit. It just makes sense that avoiding use of its military symbols fit the Jackdaw being a deep scouting vessel. You don't want people to identify Nepleslia wrongly as, say, another nation with star symbols or anchors on their crest =3=/