Both accomplish the same thing, but writing a join query gives you more flexibility, or control, than a lookup transformation (in my opinion). Plus, there are pros and cons to each. With a lookup transformation, everyting is encapsolated within SQL. Good plus. Equally, SQL also handles all the connection stuff, whereas if you an oledb source, you have write and control all the connection stuff.
So, there are tradeoffs.
I'm not an SSIS guru so someone else might tell you differently. I think you best bet is to try both and see what suits your needs the best.
Hope this helps...
Scott Klein
Author - Professional SQL Server 2005 XML
http://www.wrox.com/WileyCDA/WroxTit...764597922.html