I am working on a humanoid SCP and was wondering if it was reasonable to link it to / having it once be used by Alpha-9.
Ehh… depends on the context. Why would it be in Alpha-9? If it was just once, having such an exceptional case can make it seem like wish-fulfillment.
I don't know if it would be okay to link it to Alpha-9 in any way or if I needed to ask permission or that using the SCP with Alpha-9 would get my SCP downvote bombed.
You don't need permission, and using Alpha-9 as a namedrop shouldn't be instant-downvote material, but it really depends on why. If it was just a means of racking up coolness points, then no, don't mention Alpha-9. Your focus should be on telling a story that the audience can enjoy, not just shoving an OC into the Foundation-verse with as many coolness points as you can stick on them.
What if I want to do something akin to:
"SCP-XXXX was issued to MTF ███████-██ to test its abilities…"
I personally wouldn't, mainly because I headcanon that the Foundation would never just put an anomaly with no security or informational clearance into an MTF team that handles sensitive missions just "to test its abilities". The Foundation has much less control over an anomaly out in the field than in experimental settings.
Furthermore, not everyone is familiar with Alpha-9. If you blackbox the name, that insert seems more like a "look my humanoid was cool enough to be on an MTF" attention-grab rather than a story note that hints at at specific narrative.
Tl;Dr it depends on why you want to put Alpha-9 in there.