I had the same doubt. I've done a little research in the library bitcoinj, and I think that it is possible to use multiple wallets at the same time. I recommend you first work with a single wallet so that you can understand a little how it works the library. I leave an example:

public class MainClass {
    private static final File BLOCKCHAIN_FILE = new File("block.dat");
    private static final NetworkParameters NET_PARAMS = MainNetParams.get();

    public static void main(String[] args) throws Exception {

        List<Wallet> wallets = getWallets();
        BlockStore blockStore = new SPVBlockStore(NET_PARAMS, BLOCKCHAIN_FILE);
        BlockChain blockChain = new BlockChain(NET_PARAMS, wallets, blockStore);
        PeerGroup peerGroup = new PeerGroup(NET_PARAMS, blockChain);

        for (Wallet w : wallets) {
            peerGroup.addWallet(w);
        }

        //Starting peerGroup;
        peerGroup.startAsync();

        //Start download blockchain
        peerGroup.downloadBlockChain();
    }

    public static List<Wallet> getWallets() throws UnreadableWalletException {

        List<Wallet> wallets = new ArrayList<>();
        for (int i = 0; i < 5; i++) {
            Wallet w = Wallet.loadFromFile(new File("wallet_" + i + ".dat"), null);
            wallets.add(w);
        }

        return wallets;
    }
}

You can use bitcoinj with multiple wallets (just use peerGroup.addWallet(wallet) multiple times), but it isn't designed to scale well in such a scenario. Depending on your resources and the activity on the wallets, two, three or five wallets might work ok. But hundreds will almost certainly not work.