I dont think your doing anything wrong:
pi@noads:~ $ echo 'dhcp-option=42,11.22.33.44' | sudo tee /etc/dnsmasq.d/42-pihole-dhcp-ntp.conf
dhcp-option=42,11.22.33.44
pi@noads:~ $ sudo service pihole-FTL reload
pi@noads:~ $
dehakkelaar@laptop:~$ sudo nmap -sU -p67 --script dhcp-discover 10.0.0.2
Starting Nmap 7.40 ( https://nmap.org ) at 2019-07-17 17:55 CEST
Nmap scan report for noads.dehakkelaar.nl (10.0.0.2)
Host is up (0.0013s latency).
PORT STATE SERVICE
67/udp open dhcps
| dhcp-discover:
| DHCP Message Type: DHCPACK
| Server Identifier: 10.0.0.2
| IP Address Lease Time: 23h56m42s
| Subnet Mask: 255.255.255.0
| Broadcast Address: 10.0.0.255
| Domain Name Server: 10.0.0.2
| Domain Name: dehakkelaar.nl
| NTP Servers: 11.22.33.44
|_ Router: 10.0.0.1
MAC Address: B8:27:EB:68:xx:xx (Raspberry Pi Foundation)
Nmap done: 1 IP address (1 host up) scanned in 1.94 seconds
How have you determined this ?
And did you renew DHCP lease on the clients after adding the 42 option ?