I-539 filed; decision pending while Green card application interview is also pending

There are several questions here.

Will her visa be voided?

The visa used to enter the US is generally automatically voided under INA 222(g) if one stays past the date on one's I-94. See 9 FAM 302.1-9. However, her visa is not voided during the period a timely-filed, non-frivolous EOS/COS application is pending, so if the EOS/COS is approved, or she leaves the US while it is pending (even if it is past the date on her I-94), her visa is not voided.

See 9 FAM 302.1-9(B)(1)(c)(1):

(1) In General: For the purposes of INA 222(g), an alien who entered the United States on an NIV will be considered to have overstayed his or her period of authorized stay if:

(a) The alien remained in the United States beyond the specific date stated on the Form I-94, Arrival-Departure Record; or

(b) USCIS, an IJ, or the BIA has formally found that the alien has violated his or her status.

and 9 FAM 302.1-9(B)(1)(c)(4)(a-b):

(4) Aliens with Pending Change of Status or Extension of Status Applications: An alien is not ineligible under INA 222(g) even though the departure date on Form I-94, Arrival-Departure Record, passes, if:

(a) The alien files a timely application for extension of stay or for a change of status; and

(b) The application is subsequently approved. In addition, if an alien departs after the date on the Form I-94 passes, but before his or her application for extension or change of status has been decided by USCIS, they must be subject to a blanket exemption from INA 222(g), if the application was filed in a "timely manner" and is "nonfrivolous" in nature. [...]

So:

• if she leaves before her I-94 expires, her visa is not voided
• if she files a timely EOS/COS application, and she leaves after it is approved, before the new I-94 expires, her visa is not voided
• if she files a timely EOS/COS application, and leaves while it is pending and after her I-94 expires, her visa is not voided
• if she files a timely EOS/COS application, and leaves after it has been denied, her visa is voided

Will it affect her immigrant visa?

She should not have problems getting an immigrant visa as long as she doesn't have a ban. There is an unlawful presence ban where if she accrues 180 days of unlawful presence and then leaves the US, she triggers a 3-year ban; if she accrues 1 year of unlawful presence and then leaves the US, she triggers a 10-year ban. See 9 FAM 302.11-3. However, she does not accrue unlawful presence during the period a timely-filed, non-frivolous EOS/COS application is pending, regardless of whether it is ultimately approved, abandoned, or denied.

See 9 FAM 302.11-3(B)(1)(b)(1):

b. DHS has interpreted "period of stay authorized by the Secretary of Homeland Security," as used in this context, to include:

(1) For aliens inspected and admitted or paroled until a date specified on the Form I-94 or any extension, any period of presence in the United States up until either:

(a) the expiration of the Form I-94 (or any extension); or

(b) a formal finding of a status violation made by DHS, an IJ, or the BIA in the context of an application for any immigration benefit or in removal proceedings, whichever comes first.

and 9 FAM 302.11-3(B)(1)(b)(4):

b. DHS has interpreted "period of stay authorized by the Secretary of Homeland Security," as used in this context, to include:

(4) For aliens who have applied for extension of stay or change of nonimmigrant classification and who have remained in the United States after expiration of the From I-94 while awaiting DHS's decision, the entire period of the pendency of the application, provided that:

(a) the alien does not work unlawfully while the application is pending and did not work unlawfully prior to filing the application; and

(b) the alien did not otherwise fail to maintain his or her status prior to the filing of the application (unless the application is approved at the discretion of USCIS and the failure to maintain status is solely a result of the expiration of the Form I-94), and further provided either:

(i) that the application was subsequently approved; or

(ii) if the application was denied or the alien departed while the application was still pending, that the application was timely filed and nonfrivolous.

So:

• if she leaves before her I-94 expires, she does not accrue any unlawful presence
• if she files a timely EOS/COS application, and she leaves after it is approved, before the new I-94 expires, she does not accrue any unlawful presence
• if she files a timely EOS/COS application, and leaves while it is pending and after her I-94 expires, she does not accrue any unlawful presence
• if she files a timely EOS/COS application, and is still in the US on the date it is denied, she starts to accrue unlawful presence on the date of the denial (so she would have accrued some number of days of unlawful presence by the time she receives the denial notice). However, unlawful presence does not cause her to trigger a ban upon leaving until she has accrued 180 days of it, so she has plenty of time to leave and not trigger a ban. However, she may want to leave within 33 days of the date of denial, because since 2018, USCIS has had a policy of issuing Notices to Appear for removal proceedings to people with denied I-539 who do not leave within a 33-day period.