Can I run a single Magento for Estonia + Latvia + Lithuania?

Yes, and it’s the smart move for any Baltic-region store above €500k revenue, because all three countries share EUR currency, similar consumer behaviour, and overlapping ad markets:

• One Magento backend, 3 store views, ee, lv, lt. Shared catalogue, separate URLs (yourbrand.ee / yourbrand.lv / yourbrand.lt) or one domain with country selector.
• Per-store VAT, EE 22%, LV 21%, LT 21%. Each with its own reduced rates. Magento tax_zone rules per store.
• Per-store payment methods, EE: Bank-link + Maksekeskus + Klarna. LV: Swedbank + Citadele + Klarna. LT: Paysera (LT-native) + Swedbank + Klarna.
• Per-store shipping, Omniva + DPD + SmartPost across all three (Omniva is Baltic-wide), Itella in LV. Pickup-lockers (pakiautomaat) are huge across the Baltics, ~50% of e-commerce orders.
• Per-store language, Estonian (et), Latvian (lv), Lithuanian (lt), three unrelated languages. Plus optional Russian layer (huge in LV especially: ~30% RU-speaking).
• Per-store legal pages, Tarbijakaitse (EE), PT&AC (LV), Vártotojo apsauga (LT). GDPR is enforced by AKI (EE), DVI (LV), VDAI (LT).

Architecture: single backend with 3 store views + 3 root categories + shared catalogue. We’ve done this 5+ times. Budget 6-10 weeks for full Baltic-3 build on top of an existing EE store.