Coordinates in MSFS have been always decimal and that´s the way they are configured in addons (NAVAIDs, airports, etc). However game can translate the format so you can click at game map, note down the displayed DMS coordinates and use the website you posted for the conversion from DMS to decimal. You can also directly click on that website map to get both formats in one go. And they can be also obtained from Google Maps or Bing Maps with mouse clicks quickly and then pasted directly into game world search box.
San Francisco is 37.77029733160334, -122.41749183824811. Entering that in world search box will target to San Francisco and will display the converted coordinates as well (rounding may be applied): N37° 46’ 13.07’‘, W122° 25’ 2.97’'.
Some GPS addons support both formats, so you can enter the coordinates using the format you want. For conversion purposes in that case remember that positive values in decimal are North/East and negative values are South/West.
One of the easiest ways to get coordinates is to use Little Navmap, in case you already use that tool for planning. Simply do “Right mouse click on map → More” and you could copy the decimal coordinates from anything (a location, a waypoint, etc). The “Information box” from any asset (VORs, airports, etc) will also display decimal coordinates when you simply left click on it. You can configure the tool to display the coordinates format you want in the “Options → Units” menu.
Note: the format for game shall still use “comma” as separator for coordinates and “point” as separator for decimal digits (so as written at the top of my post). You may need to manually change this if you want to enter coordinates from Little Navmap into world box.
Cheers