There's no single, general, answer as it depend why the method/type was obsoleted.
Most [Obsolete]
attributes have a message stating why you should avoid them. They mostly fall in two groups:
There was a binding error in the API, e.g. a typo. A new API was added to correct this (and its name should be part of the description). In this case there is no problem, for a 4.3 device, to use the new API added in MonoTouch 6.x;
Apple introduced a new API and deprecated the use of an older one. In this case the description should state the new API and the iOS version where it applies. You should not use the new API (e.g. anything added in iOS 6.0) if you wish to target older devices (e.g. 5.x).
If you find [Obsolete]
method/types without any text message or when the text is not clear enough to allow you to make a clear decision please file a bug report so it can be corrected.