Well, I think the fact that the ships were used as prizes was the reason they still exist, and that three of them are still sailing and serving their purpose, so we should be glad.
What I find strange enough was that "Gorch Fock (I)" became the Soviet training ship "Tovarsihsch", while Horst Wessel became the American training ship "Eagle". So you can say for almost 50 years the two opposing super powers used more or less identical ships to train their crews and even today they still both use German sailing ships. Although the Gorch Fock (I) returned to Germany, the ex-"Padua" now "Krusenstern" is still a Russian training vessel.
Let's hope this fact will keep these ships at sea for a long time so that they might one day become as famous as the HMS Victory and the USS Constitution.
As to the problem with sailing against the wind: You're right of course, but in my opinion without a weather report it's not easy to know were the wind is coming from in SH3, so to me the immersion killer is not a problem.