you can specify in the modeller to always sync the database without asking
About windows scripts (or batch files)
Using "a script" would be possible ofcourse. However, the normal procedure is to call an argument build commandline if it's available. The developers have to include this parameter option.
When no command line option is provided and not using eclips there is an option available to launch the software via an execute command and 'hack' form states to call the build button (F5) and access the deployment menu. (e.g. using a key press script)
Sample: you can use macro's e.g. vb script to write a 'call executer' (which starts Mendix) then use key presses to navigate through the menu. (do a search on window states to set the focus the Mendix modeller.) Then use key-presses to access the menu. your keypresses to automatically go to build mda is
you can write such action from any development environment such as .NET or vbscripts or macro's. There are even out of the box programs to program keystates. (some people use this in games)
Let me know for which option you are going to choose :)