Shizuku's family used to have more money.They lived in a house, and Shizuku's father was a salaryman. When Japan's economy started to slow in 1990-1991, he lost his job and took a lower-paying job at the library to make ends meet. The family lost their house, and moved to the apartment. Shizuku's mother went back to get her master's degree to hopefully regain some of the family's lost income. Both daughters reacted to the change in opposite ways: Shizuku's sister was more of a realist, resigned herself to a fate of working part-time jobs, and saved up enough money to move out. Shizuku, who would have only been about 10 when the economic bubble burst and therefore less knowledgeable about what was going on, resorted to reading fictional books as a (subconscious) form of escapism.
Louise was Jewish. She died in the holocaust.
- We know that Nishi knew Louise in Germany many years ago. He had to leave her there, and couldn't return for many years, because of "the war". When he returned, he couldn't find Louise anywhere. The war was World War 2. Louise was Jewish (or partially Jewish, or whatever.) She died in the holocaust. (Doubles as Fridge Horror!)
- Nishi knows the truth, or at least he suspects the truth. But he doesn't mention this to Shizuku, because she's just a kid and he wants to spare her feelings.
Alternatively to the above: Louise was not Jewish, but died in a bombing raidThere's no need to assume Louise was Jewish and/or a victim of the Holocaust to account for her disappearance. World War II leveled whole cities in Germany, and Louise could have easily been among the many unidentified victims of some bombing raid or another. Large bombing raids such as those on Hamburg and Dresden left many bodies too charred or mutilated to be identified.
The grandfather clock was found in Castle Cagliostro.It's a beautiful, intricate design, so is probably worth a lot of money and tells the story of two lovers destined to be apart (not wholly dissimilar to how Lupin and Clarisse ended up). Or was built by Porco from  as a reflection of himself and Gina