It means that there are not many inns (they are like hotels) available at that location, and that the inns that are available are dirty and have fleas.. "Such as it is/was they were /are " is a common way of saying there is not a lot of something and what is available is not satisfactory.

Inn has nothing to do with the word in. It means hotel, as the other person said. "...such inns as they were", means there was not a lot of variety of inns available, and the ones that had rooms available were all dirty, flea ridden etc.