If the description says it does, then it can. Otherwise, the lowest level is assumed.
General rule for casting spells from magic items:
Some magic items allow the user to cast a spell from the item. The spell is cast at the lowest possible spell level, doesn't expend any of the user's spell slots, and requires no components, unless the item's description says otherwise.
Spell scrolls are not explicitly stated to always be at the lowest possible level for the spell. That is the default for magic items. So a "scroll of magic missile" would be a level 1 scroll and follow the table for casting an L1 scroll. However, a "scroll of magic missile level two" would be a level two spell scroll. It still fits with the general description of spell scrolls, and with magic items since the description states the spell level.
Xanathar's Guide to Everything offers guidance on the cost and nature of scribing spell scrolls. It has a table relating the level of the spell to the cost of it and the requirements on the scribe.
Following the table, scribing a 2nd level magic missile scroll would take the cost from 25gp to 250gp and doubles the required time to complete the task.