Yes, et ses amis non plus is ambiguous here.

Should you need to avoid it, you might just clarify the second part that way:

Je ne l’ai pas vu aujourd’hui. Ses amis ne l’ont pas vu non plus.

Yes, you’re right, it could have the same meaning. I would personally use this translation :

Ni moi ni mes amis ne l’avons vu aujourd’hui

to correct tense usage

Your sentence is almost correct. You can avoid ambiguity, if you remove the “et” that can give a different sense, which would give this correction:

Je ne l’ai pas vu aujourd’hui, ses amis non plus.

OU

Je ne l’ai pas vu aujourd’hui. Ses amis non plus.

If you say, “Je ne l’ai pas vu aujourd’hui, et ses amis non plus”, it’s like saying “I haven’t seen him today, such as his friends”.

Truth is, my answer is like saying:”Je ne l’ai pas vu aujourd’hui, ses amis ne l’ont pas vu non plus.” It’s just less heavier than including a verb, especially if this one can be omitted.

I hope it will help you.