The regular Ship disables battling and exploring during an upgrade (and rightfully so, since the Ship is in dock being worked on). Other buildings also disable such as the Academy, Voodoo Hut, Flame Gates... The Guild Ship however, continues to work. You can take it with you to battles and you can request pirates from your guild. Though I like the fact that this is so (as I'm rocking a level 1 Guild Ship on my second island), I consider this very much a bug. In addition to that there is inconsistency. If you can somehow justify the Guild Ship functioning during an upgrade (yeah yeah, gameplay blah blah), then there should be a Request button available when you select it (just like the Tavern mid-upgrade, but that's a different thread) instead of having to use the quick link at the top (see spoiler for screenshot). Spoiler
