Is an increase in the money supply (by buying government bonds) recorded in bank deposits or bank reserves? When the central bank pays 100 shekels for a bond held by the public, it is assumed that the 100 shekels are deposited. In this case, shouldn't it cause a 100 shekels increase in the bank deposit rather than in the bank reserve?
No. 

Think of it as the central bank is buying the bond from the commercial bank itself, so that the bank was holding one type of asset (a bond) and now it's holding another type of asset(cash or its equivalent, reserves at the central bank). At that point deposits have not increased, it's just, that the bank now is holding more cash and less bonds than before. Because cash holdings or reserves at the central bank are called 'reserves', the commercial bank's reserves have increased. 

The next step is that this bank sees no benefit in holding so much cash, more than the regulation forces it to, so ti goes and lends this cash out. At that point deposits start increasing, but still, the whole of the banking system is going to have more reserves than before because somebody is going to be holding that cash.