Dear Querist,
(i) There is not an iota of doubt that non-declaration of taxable value in GSTR-3B return amounts to suppression of facts and Section 74 is invocable as opined by Sh. Sadanand Bulbule, Sir.
(ii) However, I am also of the view that if you have recorded all the transactions in the books of account (statutory records) and have filed Income Tax Returns on the basis of the books of accounts, then you can prove your bona fides before the Appellate Authority. You can contest the invocation of Section 74 in the SCN and confirming the demand under Section 74 along with interest and penalty. There are case laws to this effect.
(iii) You are to prove non-declaration of correct taxable value as unintentional. If the element of 'willful suppression with an intent to evade tax' is absent, Section 74 cannot be invoked and if invoked, that will not be sustainable. Peruse all the ingredients mentioned in Section 74 and rebut each.
(iv) Also go through the scope of term, 'books of accounts' as detailed in the Company Act.
(v) Last but not the least, in case all your transactions are genuine, you must contest. You will have to admit the lapse occurred but lay emphasis on the fact of bona fide mistake.