Moneydance creates default locations under your home directory when it is installed.
Some files need to remain there like the configuration file and loaded extensions. There is nothing particularly confidential in these files however, your data files you can move to anywhere on your system that you like.
TiK have provided the following guide to moving data files:
Moneydance encrypts the data files by default so that only moneydance can read them and if you like you can also use your own password on these files so they cannot be opened unless you supply the password. If you use online banking you must supply your own password in order for bank site passwords to be stored in the data file.