Because the rule only applies to penalising people for past conduct. It does not mean that anything you ever bought cannot be confiscated.
Takings clause? It doesn't specify real estate (its common use) it says "private property", and since "just compensation" is pretty damn easy to determine given market values and numerous insurance cases settled by judges, it would be tough to do a confiscation. Remember, this isn't gold (that worked due to packing threats, and the fact it was actually money then, and thus market value was established, and it was an "exchange".
The government has never really been able to confiscate anything, only make its use or future production illegal or regulated (see drugs, leaded gas, Hughes amendment, etc)
If the penalty for not surrendering property is criminal, then ex post facto applies, so possession becomes a civil matter or eminent domain.
Extension of eminent domain to objects is a big stretch, and would be challenged heavily. Additionally, even if the takings clause were twisted to allow this, the .gov can simply not afford to provide fair value, and thus nearly ever case would be challenged.
Additionally could the .gov even afford it? There are 300 million firearms, even if 1/3rd are eligible, and the average price is $300-500, that's $30-50 billion, plus the economic effects of killing that industry...and the calls from those companies to their congress critters.
Molon labe.
