On the ICAO Flight Plan Form, does /S replace O, V, and L?
I wanted to address your formatting first since equipment type identifiers come before the transponder identifier (i.e. before the slant). The format for the new ICAO Domestic flight plan form for item 10 (equipment) is as follows:

(equipment type letters) / (transponder type)

So as an example, if your aircraft has standard equipment, VOR, GPS (GNSS), DME and you were Mode C Transponder equipped, your entry for item 10 would look like this: 

SGD / C 

*notice that your equipment type doesn't include "O" for VOR since S also includes VOR. 

To answer your concrete question, S does indicate the presence of O, V, and L.

I've attached the following tables from 5-1-21 and 5-1-22 in the AIM for your reference. Table 5-1-4 covers equipment letter identifiers and table 5-1-5 covers transponder letter identifiers.