You can have several copies of "NppExec.dll" in your Notepad++'es Plugins subfolder in order to have several NppExec's Console windows. Each copy of NppExec saves its own options and its own console commands history (if it is enabled in NppExec's options). In the same time, saved NppExec's scripts are shared between several copies of NppExec.
To have several copies of "NppExec.dll", just copy it with different name(s), for example, "NppExec2.dll", "NppExecCpp.dll", "NppExecWeb.dll" and so on. This will give you additional NppExec's Console windows with the corresponding titles: "Console2", "ConsoleCpp", "ConsoleWeb" and so on.
Note: in modern versions of Notepad++, each instance of NppExec.dll should be located in its own folder.
Thus, to have e.g. "NppExecCpp.dll", make a copy of the entire folder "plugins\NppExec" as "plugins\NppExecCpp" and then rename "plugins\NppExecCpp\NppExec.dll" to "plugins\NppExecCpp\NppExecCpp.dll". (Be sure that the .dll name matches the folder name!)
Also, be sure to have the inner subfolder "NppExecCpp\NppExec" (that contains "BaseDef.h", "menuCmdID.h" and so on) because each instance of NppExec.dll needs it near itself. (This inner "NppExec" subfolder should preserve its initial name).
To sum up, the following files/folders tree is expected in case of "NppExec.dll" and "NppExecCpp.dll":
plugins\ NppExec\ NppExec\ BaseDef.h menuCmdID.h Notepad_plus_msgs.h Scintilla.h NppExec.dll NppExecCpp\ NppExec\ BaseDef.h menuCmdID.h Notepad_plus_msgs.h Scintilla.h NppExecCpp.dll