Mongoコーデックを自動的に作成する方法はありますか？

これに対処する方法は次のとおりです（最終結果は、Lombok、Jackson、MongoDBの間で非常に滑らかです）：

プロバイダー：

public class JacksonCodecProvider implements CodecProvider {
    private final ObjectMapper objectMapper;

    public JacksonCodecProvider(final ObjectMapper bsonObjectMapper) {
        this.objectMapper = bsonObjectMapper;
    }

    @Override
    public <T> Codec<T> get(final Class<T> type, final CodecRegistry registry) {

            return new JacksonCodec<>(objectMapper, registry, type);

    }
}

そしてコーデック自体：

class JacksonCodec<T> implements Codec<T> {
    private final ObjectMapper objectMapper;
    private final Codec<RawBsonDocument> rawBsonDocumentCodec;
    private final Class<T> type;

    public JacksonCodec(ObjectMapper objectMapper,
                        CodecRegistry codecRegistry,
                        Class<T> type) {
        this.objectMapper = objectMapper;
        this.rawBsonDocumentCodec = codecRegistry.get(RawBsonDocument.class);
        this.type = type;
    }

    @Override
    public T decode(BsonReader reader, DecoderContext decoderContext) {
        try {

            RawBsonDocument document = rawBsonDocumentCodec.decode(reader, decoderContext);
            String json = document.toJson();
            return objectMapper.readValue(json, type);
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    @Override
    public void encode(BsonWriter writer, Object value, EncoderContext encoderContext) {
        try {

            String json = objectMapper.writeValueAsString(value);

            rawBsonDocumentCodec.encode(writer, RawBsonDocument.parse(json), encoderContext);

        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }

    @Override
    public Class<T> getEncoderClass() {
        return this.type;
    }
}

Lombokと最新のJacksonアノテーションを組み合わせると、次のようなことが可能になります（Javaコードのようには見えませんね）：

@JsonIgnoreProperties(ignoreUnknown=true)
@JsonDeserialize(builder = Account.AccountBuilder.class)
@Builder(toBuilder=true)
@Value
public class Account {

    @JsonProperty private String _id;
    @JsonProperty private long _version;
    @JsonProperty private String organizationName;

    @JsonPOJOBuilder(withPrefix = "")
    public static final class AccountBuilder {
    }

}

次に：

Account account = collection.find(eq("_id", id)).first();
System.out.println(account.getOrganizationName());