1. You can generate source maps for your TS files, but node can't use them. There is some support for source maps via the node-source-map-support, but it doesn't play well with a lot of stuff out of the box. Just getting accurate stack traces in my logs turned into a project of its own.
2. Most node libraries don't include type definitions, and what is on DefinitelyTyped is more likely than not to be out-of-date and inaccurate. Having the wrong type definitions might be worse than none at all, which means for the most part you'll be declaring a lot of stuff as "any." It makes even preserving the types in your own code difficult, as anything that touches a 3rd-party library is going to come back as the any type without additional annotation.
3. Similar to 2, if you want to use a promise-based approach to deal with the "callback hell" induced by node's continuation passing style, you are probably going to need to use a library that does runtime mutation of the many libraries that don't support promises, which means that any time information you do have about 3rd-party libraries is going to get lost.
4. The last two items, combined with the lack of runtime type checking, means that your types are going to be difficult to maintain and can easily become inaccurate without feedback from the compiler to let you know that something is wrong.