The attacks against Android might affect Maemo precisely because they share the same Linux core.
However, the actual difficulty will be with different processors/architectures.
There are different solutions:
1.Python/perl/HTML/Javascript/Java/sh/alike architecture-independent virus/trojan;
2.storing several versions on server and downloading the needed one to phone;
3.fat virus which contains versions for all the architectures.
Of course, it's difficult to build virus which would know vulnerabilities of all phones in the world. So most likely, Maemo will be left out.