I really do not see this as a bad thing but something more positive.
Think of it this way, C is a partition for the OS alone. Only windows and windows updates should go here from now on. Treat D as the storage partition, make a new folder and call it Software or Program files. It will look like this D:\Program Files\_______
and save all the programs in this location. I would then uninstall the programs and reinstall them on this new partition. That way you can clear up some room for C drive.
The advantages of this is in case you need to format, any documents, pictures, songs store on D partition would remain safe. Since you would just format and reinstall windows on C partition.
The downfalls come when you are doing system image backups and it now has to do both partitions.
Another downfall would the need to change the installation location manually every time or you could edit the registry and change to the new location. I would advise against this since editing the registry can lead to catastrophic episodes later on.
I do not think you can merge C and D, unless you delete both volumes (partitions) and then they can join together.