Conversion of docx files with Mathtype equations is not done properly (by Uploading docx to docx2Latex website)
There are some ways to fix this:

I have written a macro which converts Mathtype equations to MS word equations, then we can use Doc2Latex for conversion to Latex: https://github.com/aminya/AminMSWordVBAmacros#mathtype2word

Another way is to convert Mathtype equations to Latex inside MS word (Mathtype has a macro for this). But Doc2Latex should have some logic to detect the equations that are between
\[ \]
and$ $
, and not convert them to simple text, and instead to math equations. In Google doc addon, the user can inter Latex blocks for these, but it is timeconsuming and manual. 
Fix the direct conversion errors.
Now without any change Mathtype equations like this:
are converted to this:
Also, equations numbers are ignored which is another problem!