Background and Objectives: The aim of the study was to evaluate the predictive value of the ultrasound criterion “non-marked hypoechogenicity” for malignancy and to determine whether classification of these nodules as TIRADS 3 could improve the overall accuracy of consequently adjusted M-TIRADS score. Materials and Methods: A total of 767 patients with 795 thyroid nodules were subject to ultrasonography examination and ultrasound-guided fine needle aspiration biopsy. Nodules were classified by Kwak TIRADS and modified (M-TIRADS) categories 4A, 4B, and 5 according to number of suspicious US features (marked hypoechogenicity, microlobulated or irregular margins, microcalcifications, taller-than-wide shape, metastatic lymph nodes). Non-marked hypoechoic nodules were classified as TIRADS 3. Results: Thyroid nodules were classified as TIRADS 2, 3, 4A, 4B, and 5 in 14.5, 57.5, 14.2, 8.1, and 5.7%, respectively. Only histopathologic results (125 nodules underwent surgery) and highly specific cytology results (Bethesda II, VI) were accepted as a standard of reference, forming a sub-cohort of 562/795 nodules (70.7%). Malignancy was found in 7.7%. Overall, M-TIRADS showed sensitivity/specificity of 93.02/81.31%, and for PPV/NPV, these were 29.2/99.29%, respectively (OR—18.62). Irregular margins showed the highest sensitivity and specificity (75.68/93.74%, respectively). In TIRADS 3 category, 37.2% nodules were isoechoic, 6.6% hyperechoic, and 52.2% hypoechoic (there was no difference of malignancy risk in hypoechoic nodules between M-TIRADS and Kwak systems—0.9 vs. 0.8, respectively). Accuracy of M-TIRADS classification in this cohort was 78.26% vs. 48.11% for Kwak. Conclusions: The non-marked hypoechoic nodule pattern correlated with low risk of malignancy; classification of these nodules as TIRADS 3 significantly improved the predictive value and overall accuracy of the proposed M-TIRADS scoring with malignancy risk increase in TIRADS 4 categories by 20%; and no significant alteration of malignancy risk in TIRADS 3 could contribute to reducing overdiagnosis, obviating the need for FNA.