As you observed, Nigeria is not among the countries where Apple Pay is available
Countries and regions that support Apple Pay
Apple Pay is available in a territory only after successful business negotiations between Apple, the local Banks and government regulators. It is not up to Apple alone. If you want to express your interest in Apple Pay in Nigeria send your comments directly to Apple: Feedback - Apple Pay - Apple.
iCloud+ is available in Nigeria. The cost for an iCloud+ subscription is
50 GB: ₦900
200 GB: ₦2900
2TB: ₦9900
6TB: ₦26900
12TB: ₦44900
and you would pay for this via the payment method set in your Apple Account - not by Apple Pay.
Payment methods that you can use with your Apple Account - Apple Support (NG). This support document says that "Most credit and debit cards" are accepted.
What difficulties are you experiencing in purchasing an iCloud+ plan in Nigeria?