No, the weapons used are different and so are the damage output values. Conscripts with PPsH not only get just 2 PPsH(As opposed to Shocks getting 6), the PPsH with the Conscript upgrade is a different weapon model and puts out different damage values to the Shocktrooper PPsH.
Really, what do you want? You're paying 20 manpower to reinforce instead of 45. This is a trade off. If you have a problem with the reinforcement cost, then compromise. Otherwise, suck it up. Shocktrooper models are incredibly powerful. You pay the 480MP to get a high DPS squad on the field that has several grenade options and is initially extremely durable. You pay double the price for the impact of such a powerful unit, and then you maintain the DPS and special grenades by merging them with Conscripts. What is your problem?
i dont know about using a different weapon model, but they use the exact same stats. there actually isnt 2 files for ppsh. theres only one file named shocktroop ppsh, which the conscripts also use. youre right that cons only get 2 and shocks get 6 though.