SSIS is a terrific tool for complex ETL tasks. You can even write C# code if you need to. There are lots of pre-written available data cleaning components already out there for you to download if you want. It can pretty much do anything you need to do. It does however have a fairly steep learning curve. SSIS comes free with SQL Server so that is a plus. A couple of things I really like about SSIS are the ability to log errors and the way it handles configuration so that moving the package from the dev environment to QA and Prod is easy once you have set it up.
We have also set up a meta data database to record a lot of information about our imports such as the start and stop time, when the file was recieved, the number of records processed, types of errors etc. This has really helped us in researching data issues and has helped us write some processes that are automatically stopped when the file exceeds the normal parameters by a set amount. This is handy if you normally recive a file with 2 million records and the file comes in one day with 1000 records. Much better than delting 2,000,000 potential customer records because you got a bad file. We also now have the ability to do reporting on files that were received but not processed or files that were expected but not received. This has tremendously improved our importing porcesses (we have hundreds of imports and exports in our system). If you are designing from sratch, you might want to take some time and think about what meta data you want to have and how it will help you over time.
Now depending on your situation at work, if there is a possibility that data will also be sent to the SQL Server database from sources other than Lotus Notes as well as the imports from Notes that you are developing for, I would suggest it might be worth your time to go ahead and start using SSIS as that is how the other imports are likely to be done. As a database person, I would prefer to have all the imports I support using the same technology.
I can't say anything about DECS as I have never used it.